Project Pokémon Bot

Players receive this starter in Sun, Moon, Ultra Sun & Ultra Moon.
     Species   Litten   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   In-Game Gift   Location   Route 1USUM / Iki TownSM   Dates   (Various)   PID   Chance of Shiny   Games   SM USUM                                                                Lv. 5    Nature   Random   Ability   Blaze   Item   None    Moves   (ITALIC means Relearnable)   Scratch   Ember   Growl   (None)
  Format Ver.1.0.6-2, Post Updated Date:20180427_1721

Players receive this starter in Sun, Moon, Ultra Sun & Ultra Moon.
     Species   Popplio   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   In-Game Gift   Location   Route 1USUM / Iki TownSM   Dates   (Various)   PID   Chance of Shiny   Games   SM USUM                                                                Lv. 5    Nature   Random   Ability   Torrent   Item   None    Moves   (ITALIC means Relearnable)   Pound   Water Gun   Growl   (None)
  Format Ver.1.0.6-2, Post Updated Date:20180427_2229

Wild and Gift Zygarde only have access to the ability Aura Break. However, upon collecting a certain amount of cells (depending on existing Zygarde),
an existing Zygarde can be fused together with said cells, to obtain a Power Construct Zygarde.

Only Power Construct Zygarde are able to interchange between 10% and 50% forms.
Additionally, they gain access to the Complete Form (in-battle only form, which appears when HP drops below half).
As wild or in-game gift Zygarde in Gen 6 and 7 are unable to be obtained shiny,
the 2018 Legends: Shiny Zygarde was used for this entry.
The non-shiny Zygarde entry comes from the Resolute Cave Zygarde entry.
The summary below shows an example of the event Zygarde in Complete form.
   Species   Complete Zygarde   Nickname   (default, in )   OT   2018 Legends   TID   060218   Distribution   (Various)   Location   a lovely place   Dates   (Various)   PID   Shiny PID   Games   Ultra Sun & Ultra Moon                                                                Lv. 100    Nature   Relaxed   Ability   Power Construct (1)   Item   Gold Bottle Cap    Moves   (ITALIC means Relearnable)   Thousand Arrows   Outrage   Extreme Speed   Dragon Dance
  Format Ver.1.0.6-2, Post Updated Date:20180602_0214

A Pokémon not native to Alola. It's only appearance in the game, is during the Team Rocket's Invasion of Aether Paradise.
     Species   Electrode   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Team Rocket’s Castle   Dates   (Various)   PID   Cannot Be Shiny   Games   USUM                                                                Lv. 60    Nature   Random   Ability   Soundproof (1)   Item   None    Moves   (ITALIC means Relearnable)   Discharge   Explosion   Gyro Ball   Mirror Coat
  Format Ver.1.0.6-2, Post Updated Date:20180702_1733

In Pokemon Black 2 & White 2, after the player has seen every Pokemon in the New Unova Pokedex,
Professor Juniper gives the player a Permit, which grants player access to the Nature Preserve.
The Nature Preserve is accessible via plane from Mistralton City.

The Nature Preserve is home to many high leveled Pokemon, and also a rare Shiny Haxorus.
     Species   Haxorus   Nickname   (default, in )   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Nature Preserve   Dates   (Various)   PID   Shiny PID   Games   Black 2 & White 2                                                                Lv. 60    Nature   Random   Ability   Rivalry (1) 
or Mold Breaker (2)   Item   None    Moves       Taunt   Dragon Pulse   Swords Dance   Guillotine
  Format Ver.1.0.6-1, Post Updated Date:20180222_0015

In Pokemon White 2, after the player defeats Benga at the White Treehollow in the White Forest,
Benga returns to Alder's house, and will give the player a Shiny Dratini.
     Species   Dratini   Nickname   (default, in )   OT   (recipient)   TID   (recipient)   Distribution   In-Game Gift   Location   Floccesy Town   Dates   (Various)   PID   Shiny PID   Games   White 2                                                                Lv. 1    Nature   Random   Ability   Shed Skin   Item   Exp. Share    Moves       Wrap   Leer   (None)   (None)
  Format Ver.1.0.6-1, Post Updated Date:20180222_0206

In Pokemon Black 2, after the player defeats Benga at the Black Tower in the Black City,
Benga returns to Alder's house, and will give the player a Shiny Gible.
     Species   Gible   Nickname   (default, in )   OT   (recipient)   TID   (recipient)   Distribution   In-Game Gift   Location   Floccesy Town   Dates   (Various)   PID   Shiny PID   Games   Black 2                                                                Lv. 1    Nature   Random   Ability   Sand Veil   Item   Exp. Share    Moves       Tackle   (None)   (None)   (None)
  Format Ver.1.0.6-1, Post Updated Date:20180222_0213

In Pokémon Black 2 & White 2, a new feature called Hidden Grottoes were introduced. In these spots, besides random item spawns, players get to encounter Pokémon that have their Hidden Ability, which cannot be normally found in standard grass/cave/water encounters in the games. The levels varies, depending on which Grotto the Pokémon was encountered in. It is important to note that any kind of Hidden Grotto encounter cannot be shiny.

Besides the standard grotto encounters, the in-game mechanic Funfest Missions also allows for different Pokémon to be encountered, though all but one of such mission are local wireless missions.

This page hosts files of the various different species that can encountered in the standard grotto, as well as Funfest Mission grottoes.
To be completely transparent, the Funfest grotto encounters were obtained using RAM manipulation, as detailed here. The only reason why this is done and why the files are included, is because it appears the encounters generated are indistinguishable from the actual Funfest mission.
Poliwag has been removed, because there's an announcement that claims the announcement for Poliwag was a mistake, and wouldn't be included.

In Pokemon HeartGold & SoulSilver, when players bring an event Fateful Encounter Arceus to the Ruins of Alph,
the player will get transported to the Sinjoh Ruins, and get to choose to receive a Dialga, Palkia or Giratina.
Each of them will come with their respective power orbs, and this is the only way to obtain the Griseous Orb in Pokemon HeartGold & Soulsilver, as the item cannot be traded.

While impossible to obtain legitimately, a Hall of Origin Arceus would allow the player to return to the Sinjoh Ruins once last time via the Ruins of Alph.
     Species   Dialga   Nickname   (default, in )   OT   (recipient)   TID   (recipient)   Distribution   In-Game Gift   Location   Sinjoh Ruins   Dates   (Various)   PID   Chance of Shiny   Games   HeartGold & SoulSilver                                                                Lv. 1    Nature   Random   Ability   Pressure   Item   Adamant Orb    Moves       Dragon Breath   Scary Face   (None)   (None)
  Format Ver.1.0.6-1, Post Updated Date:20180221_0753

In Pokemon HeartGold & SoulSilver, when players bring an event Fateful Encounter Arceus to the Ruins of Alph,
the player will get transported to the Sinjoh Ruins, and get to choose to receive a Dialga, Palkia or Giratina.
Each of them will come with their respective power orbs, and this is the only way to obtain the Griseous Orb in Pokemon HeartGold & Soulsilver, as the item cannot be traded.

While impossible to obtain legitimately, a Hall of Origin Arceus would allow the player to return to the Sinjoh Ruins once last time via the Ruins of Alph.
     Species   Palkia   Nickname   (default, in )   OT   (recipient)   TID   (recipient)   Distribution   In-Game Gift   Location   Sinjoh Ruins   Dates   (Various)   PID   Chance of Shiny   Games   HeartGold & SoulSilver                                                                Lv. 1    Nature   Random   Ability   Pressure   Item   Lustrous Orb    Moves       Dragon Breath   Scary Face   (None)   (None)
  Format Ver.1.0.6-1, Post Updated Date:20180221_0800

In Pokemon HeartGold & SoulSilver, when players bring an event Fateful Encounter Arceus to the Ruins of Alph,
the player will get transported to the Sinjoh Ruins, and get to choose to receive a Dialga, Palkia or Giratina.
Each of them will come with their respective power orbs, and this is the only way to obtain the Griseous Orb in Pokemon HeartGold & Soulsilver, as the item cannot be traded.

While impossible to obtain legitimately, a Hall of Origin Arceus would allow the player to return to the Sinjoh Ruins once last time via the Ruins of Alph.
   Species   Giratina (Origin)   Nickname   (default, in )   OT   (recipient)   TID   (recipient)   Distribution   In-Game Gift   Location   Sinjoh Ruins   Dates   (Various)   PID   Chance of Shiny   Games   HeartGold & SoulSilver                                                                Lv. 1    Nature   Random   Ability   Levitate   Item   Griseous Orb    Moves       Dragon Breath   Scary Face   (None)   (None)
  Format Ver.1.0.6-1, Post Updated Date:20180221_0759

In Pokemon HeartGold & SoulSilver, when players bring a Shiny Fateful Encounter Pichu/Pikachu/Raichu in the lead to the shrine in Ilex Forest,
Spiky-eared Pichu would appear and play with the player's Pokemon, and subsequently join the player's team.

It's normally impossible to obtain more than one Spiky-eared Pichu, as it cannot be traded,
and it also cannot be transferred to future generations.

Data below refers to the file on this page.
     Species   Pichu (Spiky-eared)   Nickname   (default, in )   OT   N   TID   00002   Distribution   In-Game Encounter   Location   Ilex Forest   Dates   (Various)   PID   Cannot Be Shiny   Games   HeartGold & SoulSilver                                                                Lv. 30    Nature   Naughty   Ability   Static (1)   Item   Zap Plate    Moves       Helping Hand   Volt Tackle   Swagger   Pain Split
  Format Ver.1.0.6-1, Post Updated Date:20180221_0820

In Pokemon HeartGold & SoulSilver, after completing the Master's Quiz with the correct answers,
the player will receive a Dratini with the move Extreme Speed.
     Species   Dratini   Nickname   (default, in )   OT   (recipient)   TID   (recipient)   Distribution   In-Game Gift   Location   Dragon's Den   Dates   (Various)   PID   Chance of Shiny   Games   HeartGold & SoulSilver                                                                Lv. 15    Nature   Random   Ability   Shed Skin   Item   None    Moves       Extreme Speed   Thunder Wave   Twister   Dragon Rage
  Format Ver.1.0.6-1, Post Updated Date:20180222_2149

Every Friday, in Pokemon Diamond, Pearl & Platinum, a wild Drifloon will appear in the over-world as a stationary encounter.
However, it will not show up on the Friday that the player ended Team Galactic's occupation of Valley Windworks.

Presently, this page holds the Drifloon that was captured on Pokemon Platinum.
(the shiny file was obtained via abusing the Cute Charm mechanic)
   Species   Drifloon   Nickname   (default, in )   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Valley Windworks   Dates   (Various)   PID   Chance of Shiny   Games   Platinum                                                                Lv. 15    Nature   Random   Ability   Aftermath (1) 
or Unburden (2)   Item   None    Moves       Minimize   Astonish   Gust   Focus Energy
  Format Ver.1.0.6-1, Post Updated Date:20180223_1049

In Pokemon Platinum, Giratina can be encountered and captured when Cyrus's plans at the Spear Pillar falls through (and he, into the Distortion World).
If Giratina was not captured at the Distortion World, it can be encountered again after the player enters the Hall of Fame, at the Turnback Cave.
The Giratina from this second (and subsequent) encounter will not have any level boost from the first,
with the only notable difference being that Giratina no longer being in it's Origin forme.

The Griseous Orb that allows it to morph into it's Origin forme can only be obtained,
after the player heads to the Turnback Cave and accesses the portal that provides access to the Distortion World.
     Species   Giratina (Altered)   Nickname   (default, in )   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Distortion World 
or Turnback Cave   Dates   (Various)   PID   Chance of Shiny   Games   Platinum                                                                Lv. 47    Nature   Random   Ability   Pressure   Item   None    Moves       Ominous Wind   Ancient Power   Dragon Claw   Shadow Force
  Format Ver.1.0.6-1, Post Updated Date:20180223_1105

In Pokemon Diamond, Pearl & Platinum, Heatran appears in Stark Mountain after the Magma Stone was moved.

In Pokemon Diamond & Pearl, Buck is responsible for it's appearance. Talking to Buck in the Survival Area to lead to the return of the Magma Stone, and Heatran will then appear in the final chamber.
In Pokemon Platinum, Charon attempts to steal the stone but gets stopped by Looker, and Buck returns the stone immediately.
However, Heatran will only appear after the player speaks to Buck in the Battleground in the Survival Area.

The file on this page consists of the Heatran captured in Pokemon Platinum.
It was possible to obtain the shiny Heatran via abusing the Cute Charm mechanic, as it can randomly be male or female.
   Species   Heatran   Nickname   (default, in )   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Stark Mountain   Dates   (Various)   PID   Chance of Shiny   Games   Platinum                                                                Lv. 50    Nature   Random   Ability   Flash Fire (1 or 2)   Item   None    Moves       Metal Sound   Crunch   Scary Face   Lava Plume
  Format Ver.1.0.6-1, Post Updated Date:20180223_2355

When the absolute difference between the player's Trainer ID and Secret ID is rather small (approximately less than 230)
and has a Pokemon with the Cute Charm ability (of a select gender) in the lead of the party (ie. a Cleffa),
shiny odds can be increased up to 21.34%, as long as the wild Pokemon species has a gender ratio that allows it to be male or female.
This particular abuse of the Cute Charm mechanic only works in Gen IV.
 
This page holds all the Shiny Pokemon I came across during my playthrough, that appear thanks to the Cute Charm abuse.
Each set that I upload will be unique (meaning a new set won't have stuff that I uploaded in a previous set)
Presently there's only three sets.
Set 08 May 18
Set 08 March 19 (ver 2)
Set 09 March 19
Set 10 March 19

Note: This isn't a request page. I'm uploading what I chance upon, and won't go out of my way to get more.
 
Other userful information:
@KazoWAR's explainer video.
Smogon's TID-SID and Party Lead's Gender table:

Presently, the only Manaphy that can be shiny, is the hatched Manaphy egg from Pokémon Ranger.
However, the received egg is shiny-locked. The only way the egg can be shiny, is if the egg was traded.
At that point, the player is subject to the standard RNG, in terms of trying to match the Egg Shiny Value (ESV) [based on PID] to the traded trainer's Trainer Shiny Value [based on TID and SID].

Another quirk regarding trading eggs to hatch them shiny, is that they will not be shiny in the hatching animation, but will be shiny in the summary.
This is because the original trainer's TID and SID is on the egg, and the hatching animation used that TID/SID, instead of the hatcher's TID/SID.

In Pokémon Crystal, lies an event encounter whereby users get to challenge (and potentially capture) the Mythical Celebi.
Problem is, the encounter required the usage of the Mobile Communication Device, that was scrapped from the International Versions of the game.
As such, this event became unused for a good 10 odd years. (Using the cheat code 91C089DA, players can immediately get the GS BALL from Kurt, and proceed to get the encounter.)
 
As of 26th January 2018 12AM (Australia time), Pokémon Crystal (international versions) has been released to the Virtual Console,
with the only requirement for obtaining it being defeating the Elite Four. (Any instance would unlock the flag. Any other step, such as bringing the GS Ball to Kurt and waiting for one day still applies.)
This allowed Celebi to be legitimately captured and transferred up to generation 7.

This file was first uploaded to our Unreleased Gallery, as the Celebi event was unused at that point in time.
This page hosts the Celebi, obtained from the encounter.

The details below reflect the encounter, not the file itself.
   Species   Celebi   Nickname   (default, in )   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   the Johto region   Dates   (Various)   PID   Chance of Shiny PID   Games   VC Crystal                                                                Lv. 30    Nature   Random   Ability   Natural Cure (1)   Item   None    Moves   (ITALIC means Relearnable)   Heal Bell   Safeguard   Ancient Power   Future Sight
  Format Ver.1.0.6-0, Post Updated Date:20180126_0156
(Inside the Spoiler, shows GIFs detailing the encounter)

It's possible to use some glitches to obtain it, as seen here, from Chickasaurus' video:

One of the legendary beasts that roams Johto. Legend has it, that it's presence can instantly purify filthy, murky water.
Apparently, Suicune only has access to Water Gun in Gold and Silver.
 
 Species   Suicune   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   Roaming Johto   Location   the Johto region   Dates   (Various)   PID   Chance of Shiny   Games   VC GS    Lv. 40                                                                  Nature   Random   Ability   Inner Focus (HA)   Item   None   Bundled Item   None 
    Moves   (ITALIC means Relearnable)   Leer   Water Gun   Roar   Gust Details above depicts one caught by a player, not fully representative of this file.

One of the legendary beasts that roams Johto. Legend has it, that one is born every time a volcano appears.
 
 Species   Entei   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   Roaming Johto   Location   the Johto region   Dates   (Various)   PID   Chance of Shiny   Games   VC GS    Lv. 40                                                                  Nature   Random   Ability   Inner Focus (HA)   Item   None   Bundled Item   None 
    Moves   (ITALIC means Relearnable)   Leer   Ember   Roar   Fire Spin Details above depicts one caught by a player, not fully representative of this file.

One of the legendary beasts that roams Johto. Legend has it, that the rain clouds it carries lets it fire thunderbolts at will.
 
 Species   Raikou   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   Roaming Johto   Location   the Johto region   Dates   (Various)   PID   Chance of Shiny   Games   VC GS    Lv. 40                                                                  Nature   Random   Ability   Inner Focus (HA)   Item   None   Bundled Item   None 
    Moves   (ITALIC means Relearnable)   Leer   Thunder Shock   Roar   Quick Attack Details above depicts one caught by a player, not fully representative of this file.

One of the legendary birds that resides in Johto. Legend has it, it continuously flies the world's skies on its magnificent seven-colored wings.
Apparently, Ho-Oh lost access to Swift from Generation V and onwards.
 
 Species   Ho-Oh   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   Tin Tower   Location   the Johto region   Dates   (Various)   PID   Chance of Shiny   Games   VC Gold    Lv. 40                                                                  Nature   Random   Ability   Regenerator (HA)   Item   None   Bundled Item   None 
    Moves   (ITALIC means Relearnable)   Sacred Fire   Safeguard   Gust   Recover  Species   Ho-Oh   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   Tin Tower   Location   the Johto region   Dates   (Various)   PID   Chance of Shiny   Games   VC Silver    Lv. 70                                                                  Nature   Random   Ability   Regenerator (HA)   Item   None   Bundled Item   None 
    Moves   (ITALIC means Relearnable)   Recover   Fire Blast   Sunny Day   Swift Details above depicts one caught by a player, not fully representative of this file.

One of the legendary birds that resides in Johto. Legend has it, that it chooses to spend its time deep at the bottom of the sea, as its wings pack devastating power that can blow apart regular houses.
Apparently, Lugia lost access to Swift from Generation V and onwards.
 
 Species   Lugia   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   Whirl Islands   Location   the Johto region   Dates   (Various)   PID   Chance of Shiny   Games   VC Silver    Lv. 40                                                                  Nature   Random   Ability   Multiscale (HA)   Item   None   Bundled Item   None 
    Moves   (ITALIC means Relearnable)   Aeroblast   Safeguard   Gust   Recover  Species   Lugia   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   Whirl Islands   Location   the Johto region   Dates   (Various)   PID   Chance of Shiny   Games   VC Gold    Lv. 70                                                                  Nature   Random   Ability   Multiscale (HA)   Item   None   Bundled Item   None 
    Moves   (ITALIC means Relearnable)   Recover   Hydro Pump   Rain Dance   Swift Details above depicts one caught by a player, not fully representative of this file.

A Pokemon that was artificially forced to evolve by Team Rocket. Huge and vicious, it is capable of destroying entire cities in a rage.
 
 Species   Gyarados   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   Lake of Rage   Location   the Johto region   Dates   (Various)   PID   Shiny PID   Games   Received in GS/C    Lv. 30                                                                  Nature   Random   Ability   Moxie (HA)   Item   None   Bundled Item   None 
    Moves   (ITALIC means Relearnable)   Thrash   Bite   Dragon Rage   Leer Details above depicts one caught by a player, not fully representative of this file.
If transferred from VC RBYG, it'll instead state the Kanto Region.