theSLAYER

In Pokémon White, if the player doesn't capture Zekrom at N's Castle, due to having a full party and full PC Box,
Zekrom can be encountered at the highest level of the Dragonspiral Tower after becoming Champion.
In Pokémon Black 2, after the player defeats N in the ruins of N's Castle, the player will be given a Dark Stone.
When the Dark Stone is brought to the peak of the Dragonspiral Tower, Zekrom will awaken, and can be challenged to a battle.

Zekrom cannot be encountered shiny in Generation 5.

In Pokemon Black & White, after players receive the event Liberty Ticket, players are able to visit the Liberty Garden.
A Shiny Victini encounter is not possible.
     Species   Victini   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Liberty Garden   Dates   (Various Dates)   PID   Cannot Be Shiny   Games   Black & White                                                                Lv. 15    Nature   Random   Ability   Victory Star   Item   None    Moves       Confusion   Incinerate   Quick Attack   Endure
  Format Ver.1.0.6-2, Post Updated Date:20180514_0929

In Pokemon Black & White, when the player brings a Movie Shiny Legendary Beast transferred up using the Relocator,
the weird camper lady in the Lostlorn Forest will attack, and take the form of a Legendary Beast.
When it takes damage, the Illusion will unravel, and reveal it was Zoroark in disguise all along.
This Zoroark cannot be encountered shiny.
     Species   Zoroark   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Lostlorn Forest   Dates   (Various Dates)   PID   Cannot Be Shiny   Games   Black & White                                                                Lv. 25    Nature   Random   Ability   Illusion   Item   None    Moves       Fury Swipes   Feint Attack   Scary Face   Taunt
  Format Ver.1.0.6-2, Post Updated Date:20180514_1056

In Pokemon Black & White, when the player brings a Gen IV Fateful Encounter Celebi transferred up using the Relocator,
and brings it to the GameFreak Building at Castelia City, the lost boy at the lobby will turn out to be a Zorua when spoken to,
and the Zorua will join the player's party.
The player gets to choose which ball to keep the Zorua in.
     Species   Zorua   Nickname   (default, in )   OT   (recipient)   TID   (recipient)   Distribution   In-Game Gift   Location   Castelia City   Dates   (Various)   PID   Cannot Be Shiny   Games   BW                                                                Lv. 10    Nature   Random   Ability   Illusion (1)   Item   None    Moves       Scratch   Leer   Pursuit   Fake Tears
  Format Ver.1.0.6-3, Post Updated Date:20180805_2342

Countless charred remains mar the landscape of places through which Thundurus has passed.
In Pokémon White, after obtaining the 8th Gym Badge then entering Route 10's Gate,
the player will be notified by the attendant that Route 7 is experiencing a bad storm.
Upon reaching a house along Route 7, the old lady will share the story regarding the Unova Roamer,
and the Roaming Encounter will be activated.

Details below refer to the gift itself, not the file.
     Species   Turtwig   Nickname   (default, in )   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Route 201   Dates   (Various)   PID   Chance of Shiny   Games   DP/Pt                                                                Lv. 5    Nature   Random   Ability   Overgrow   Item   None    Moves       Tackle   Withdraw   (None)   (None)
  Format Ver.1.0.6-2, Post Updated Date:20180424_2050

Details below refer to the gift itself, not the file.
     Species   Chimchar   Nickname   (default, in )   OT   (recipient)   TID   (recipient)   Distribution   In-Game Gift   Location   Route 201   Dates   (Various)   PID   Chance of Shiny   Games   DP/Pt                                                                Lv. 5    Nature   Random   Ability   Blaze    Item   None    Moves       Scratch   Leer   (None)   (None)
  Format Ver.1.0.6-2, Post Updated Date:20180424_2052

Details below refer to the gift itself, not the file.
     Species   Piplup   Nickname   (default, in )   OT   (recipient)   TID   (recipient)   Distribution   In-Game Gift   Location   Route 201   Dates   (Various)   PID   Chance of Shiny   Games   DP/Pt                                                                Lv. 5    Nature   Random   Ability   Torrent (1)   Item   None    Moves       Pound   Growl   (None)   (None)
  Format Ver.1.0.6-2, Post Updated Date:20180424_2102

Details below refer to the gift itself, not the file.
     Species   Rotom   Nickname   (default, in )   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Old Chateau   Dates   (Various)   PID   Chance of Shiny   Games   DP/Pt                                                                Lv. 20    Nature   Random   Ability   Levitate   Item   None    Moves       Thunder Shock   Confuse Ray   Uproar   Double Team
  Format Ver.1.0.6-2, Post Updated Date:20180424_2135

Tornadus expels massive energy from its tail, causing severe storms. Its power is great enough to blow houses away.
In Pokémon Black, after obtaining the 8th Gym Badge then entering Route 10's Gate,
the player will be notified by the attendant that Route 7 is experiencing a bad storm.
Upon reaching a house along Route 7, the old lady will share the story regarding the Unova Roamer,
and the Roaming Encounter will be activated.

In Kanto, a Snorlax blocks the entrance to Diglett's Cave, as well as the path towards to Route 11.
If defeated here, it'll appear again at Route 12 after the player enters the Hall of Fame again.
     Species   Snorlax   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Route 11 / Route 12   Dates   (Various)   PID   Chance of Shiny   Games   Heart Gold / Soul Silver                                                                Lv. 50    Nature   Random   Ability   Immunity or Thick Fat   Item   Leftovers    Moves       Block   Rollout   Crunch   Giga Impact
  Format Ver.1.0.6-2, Post Updated Date:20180507_1208

The monster that resides in the furthest reaches of the unknown dungeon.
     Species   Mewtwo   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Cerulean Cave   Dates   (Various)   PID   Chance of Shiny   Games   HeartGold & SoulSilver                                                                Lv. 70    Nature   Random   Ability   Pressure   Item   None    Moves       Psycho Cut   Amnesia   Power Swap   Guard Swap   Format Ver.1.0.6-2, Post Updated Date:20180507_1927

In Pokemon Diamond, Pearl and Platinum Versions, holds the event location Newmoon Island.

After using the event item Member Card, players gain access to the defunct Harbor Inn in Canalave City,
falls asleep enters a "dream state", dreaming of an encounter with Darkrai at Newmoon Island.
Darkrai can be captured in the "dream". If defeated or fled from, it can be re-battled again in the actual location.
The Member Card event key item was only distributed to Pokemon Platinum.
     Species   Darkrai   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Newmoon Island   Dates   (Various)   PID   Chance of Shiny   Games   Platinum                                                                Lv. 50    Nature   Random   Ability   Bad Dreams   Item   None    Moves       Hypnosis   Feint Attack   Nightmare   Double Team
  Format Ver.1.0.6-2, Post Updated Date:20180508_0013

In Pokemon Diamond, Pearl and Platinum Versions, holds the event locations Seabreak Path and Flower Paradise.
After using the event item Oak's Letter, Route 224 gains an extension (Seabreak Path) which will lead the player to Flower Paradise.
There, players will be able to challenge (and potentially capture) a level 30 wild Shaymin.
The Oak's Letter event key item was only distributed to Pokemon Platinum.
     Species   Shaymin   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Flower Paradise   Dates   (Various Dates)   PID   Chance of Shiny   Games   Platinum                                                                Lv. 30    Nature   Random   Ability   Natural Cure   Item   None    Moves       Growth   Magical Leaf   Leech Seed   Synthesis
  Format Ver.1.0.6-2, Post Updated Date:20180508_0038

From the forces of lightning and wind, it creates energy to give nutrients to the soil and make the land abundant.
In Pokémon Black & White, when the player brings both Tornadus and Thundurus to the Abundant Shrine,
Landorus will be there as a stationary encounter.

When a Pokemon Diamond, Pearl or Platinum game is launched on the NDS with a Generation III game in the slot-2, extra Pokemon encounters are unlocked in various routes, depending on the cartridge inserted.

The shiny versions of the Pokemon are also attached, if I happened to chance upon them while Cute Charm abusing.
Ruby Sapphire FireRed LeafGreen Emerald All Seedot Lotad Caterpie Weedle Teddiursa Haunter -Pt Nuzleaf Lombre Metapod Kakuna Ursaring Gengar Mawile Sableye Ekans Sandshrew Pineco Staravia -Pt Zangoose Seviper Arbok Sandslash Gligar -Pt Bibarel -Pt Solrock Lunatone Growlithe Vulpix Shuckle             Elekid -Pt Magby -Pt         -Pt means that these encounters were unavailable to Pokemon Platinum

In Pokemon Diamond, Pearl & Platinum, when the player brings Regirock, Regice & Registeel to the immobile statue at the lowest level of the Snowpoint Temple, the statue will reanimate and reveal its true identity: Regigigas.
     Species   Regigigas   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Snowpoint Temple   Dates   (Various)   PID   Chance of Shiny   Games   DPPt                                                                Lv. 1    Nature   Random   Ability   Slow Start   Item   None    Moves       Dizzy Punch   Knock Off   Confuse Ray   Foresight
  Format Ver.1.0.6-2, Post Updated Date:20180510_1727

In Pokemon Platinum, when players bring an event Regigigas to an empty cave that is in the middle of Route 228,
the normally empty cave would instead become some kind of ruins, with a statue against the wall to the end.

After stepping on all the flashing dots on the floor, Regirock will appear when the player interacts with the statue.
     Species   Regirock   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Rock Peak Ruins   Dates   (Various)   PID   Chance of Shiny   Games   Platinum                                                                Lv. 30    Nature   Random   Ability   Clear Body   Item   None    Moves       Stomp   Rock Throw   Curse   Superpower
  Format Ver.1.0.6-2, Post Updated Date:20180510_2100

In Pokemon Platinum, when players bring an event Regigigas to an empty cave in Mt Coronet that is near the exit to Route 216,
the normally empty cave would instead become some kind of ruins, with a statue against the wall to the end.

After stepping on all the flashing dots on the floor, Regice will appear when the player interacts with the statue.
     Species   Regice   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Iceberg Ruins   Dates   (Various)   PID   Chance of Shiny   Games   Platinum                                                                Lv. 30    Nature   Random   Ability   Clear Body   Item   None    Moves       Stomp   Icy Wind   Curse   Superpower
  Format Ver.1.0.6-2, Post Updated Date:20180510_2115

In Pokemon Platinum, when players bring an event Regigigas to an empty cave right near the second exist of Iron Island,
the normally empty cave would instead become some kind of ruins, with a statue against the wall to the end.

After stepping on all the flashing dots on the floor, Registeel will appear when the player interacts with the statue.
     Species   Registeel   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Iron Ruins   Dates   (Various)   PID   Chance of Shiny   Games   Platinum                                                                Lv. 30    Nature   Random   Ability   Clear Body   Item   None    Moves       Stomp   Metal Claw   Curse   Superpower
  Format Ver.1.0.6-2, Post Updated Date:20180510_2126

Its head sprouts horns as sharp as blades. Using whirlwind-like movements, it confounds and swiftly cuts opponents.
In Pokémon Black & White, after the player obtains Cobalion, an area in the Pinwheel Forest opens up, known as the Rumination Field.
There, Virizion can be found as a stationary encounter.

In Pokemon Diamond, Pearl & Platinum, not every Honey Tree is capable of yielding Munchlax.
Based on the player's Trainer ID and Secret ID, only 4 out of 21 Honey Trees will spawn Munchlax.
Even then, the encounter rate is only 1%.
Spawns only occur 6 hours after the honey is spread, and changing the NDS clock will not make it spawn faster.
Furthermore, players are not able to soft reset in terms of changing the species; other details can be SR'd.
     Species   Munchlax   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Honey Trees   Dates   (Various)   PID   Chance of Shiny   Games   DPPt                                                                Lv. 5    Nature   Random   Ability   Pickup (1) or Thick Fat (2)  Item   Leftovers    Moves       Metronome   Odor Sleuth   Tackle   Defense Curl
  Format Ver.1.0.6-2, Post Updated Date:20180511_2343

In Pokemon Diamond, Pearl & Platinum, players come across a hallowed tower made of stone at Route 209.
The player is able to fit an Odd Keystone onto the tower, and nothing else happens, normally.

If the player speaks to 32 different players (not NPC) in the Sinnoh underground,
or exit and re-enter the Sinnoh Underground multiple times after each interaction with the same person,
then finally return to the Hallowed Tower, a Spiritomb would attack.
     Species   Spiritomb   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Route 209   Dates   (Various)   PID   Chance of Shiny   Games   DPPt                                                                Lv. 25    Nature   Random   Ability   Pressure   Item   None    Moves       Feint Attack   Hypnosis   Dream Eater   Ominous Wind
  Format Ver.1.0.6-2, Post Updated Date:20180512_0018

In Pokemon HeartGold & SoulSilver, lies a chamber with a Moltres taking up residence.
     Species   Moltres   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution   In-Game Encounter   Location   Mt. Silver Cave   Dates   (Various)   PID   Chance of Shiny   Games   HeartGold & SoulSilver                                                                Lv. 50    Nature   Random   Ability   Pressure   Item   None    Moves       Ancient Power   Flamethrower   Safeguard   Air Slash
  Format Ver.1.0.6-2, Post Updated Date:20180512_0647

The final boss monster in the game, hiding in an "unknown dungeon", with it's lore being foreshadowed throughout the game.
In an environment where Psychic types are arguably overpowered, with no Dark and Steel -types to resist it, it's only weakness, is a 11 year old kid with infinite Master Balls.
 
 Species   Mewtwo   Nickname   (default, save lang)   OT   (recipient)   TID   (recipient)   Distribution    Cerulean Cave   Location   the Kanto region   Dates   (Various)   PID   Chance of Shiny   Games   VC RBY    Lv. 70                                                                  Nature   Random   Ability   Unnerve (HA)   Item   None   Bundled Item   None 
    Moves   (ITALIC means Relearnable)   Swift   Psychic   Barrier   Recover Details above depicts one caught by a player, not fully representative of this file.
If transferred from VC GS, it'll instead state the Johto Region.