Project Pokémon Bot

Scattered across the game in Pokemon XD: Gale of Darkness, there are Pokemon that are not obtainable,
including Bonsly and Munchlax, that appears early, ahead of their generation.
These Pokemon are obtained by @jojo12100, and this listing includes:
Salamence in the game's opening Metagross in the game's opening Bingo's Bonsly Battle CD's Mew Beta Starter Jolteon Beta Starter Vaporeon Proto Geodude  
Original Thread:

The Wishing Star Jirachi (Negaiboshi Jirachi) was distributed to players in Japan, with a couple of different distribution periods across the years.

The original distribution was to promote M06: Jirachi: Wish Maker, and subsequent distributions were for Pokémon Festa 2003, the 18th World Hobby Fair,
and also for the participants in lucky draw for the September 2003 issue of CoroCoro.

In Pokemon Ultra Sun and Ultra Moon, after the player earns the top spot in the leader-board, of all 4 surfing spots in Alola,
the Surfer's Association at Heahea City will give a special Pikachu that has the move surf.

The gift itself has a chance of being shiny.
The details below refer to this specific file.
 Species   Pikachu   Nickname   (default, in )   OT   PPorg   TID   171117   Distribution   In-Game Gift   Location   Heahea City   Dates   Nov 18, 2017   PID   Cannot Be Shiny   Games   US    Lv. 40                                                                  Nature   Bold   Ability   Static (2)   Item   Gold Bottle Cap 
    Moves   (ITALIC means Relearnable)   Nuzzle   Discharge   Slam   Surf Format Ver.1.0.5-5, Post Updated Date:20171116_0815

This is the first round of Birthday Events for Generation VIII, and it was distributed to players who went to Pokemon Center stores in Japan (thus JP in the title)
during the duration of their birthday month.

Identification would have to be presented upon redemption, and travelers can do so by showing their passport.

Starting February 12, 2020, the JP Birthday distributed as static PID of 06080E2F.
(Before, the PID was random, but unable to be shiny).

   Wonder Card ID #0101: Happy Birthday!  Species   Pikachu   TID   191115   Distribution   Serial Code   Location   a Pokémon Center   Dates   Nov 15, '19 to Jan 31, '21   PID   Specified: 06080E2F 
Not Shiny   Games   SWSH   Nature   Serious   Ability   Static (1)   Item   None    IVs   EVs HP ALL
RND   ALL
0 ATK DEF S.ATK S.DEF SPE
  Lv. 5       Moves   (ITALIC means Relearnable)   Celebrate   Play Nice   Thunder Shock   Quick Attack

Birthday Ribbon  Lang
 Slot    Mon's
 Lang    Nickname    OT Name   OT's 
Lang   JPN      (default name)    ポケセン    JPN  ENG      (default name)    ポケセン    JPN  FRE      (default name)    ポケセン    JPN  ITA      (default name)    ポケセン    JPN  GER      (default name)    ポケセン    JPN  SPA      (default name)    ポケセン    JPN  KOR      (default name)    ポケセン    JPN  CHS      (default name)    ポケセン    JPN  CHT      (default name)    ポケセン    JPN Only One Redemption Allowed  Format Ver.2.0.0-11b, Post Updated Date:20201101_2105

In Pokemon Ultra Sun, as part of the post game, the player gets to encounter 2 Blacephalon at the Poni Grove.

These encounters can be shiny.
The details below refer specifically to this file.
 Species   Blacephalon   Nickname   (default, in )   OT   PPorg   TID   171117   Distribution   In-Game Encounter   Location   Poni Grove   Dates   Nov 19, 2017   PID   Cannot Be Shiny   Games   US    Lv. 60                                                                  Nature   Lonely   Ability   Beast Boost (1)   Item   None 
    Moves   (ITALIC means Relearnable)   Fire Blast   Shadow Ball   Trick   Mind Blown Format Ver.1.0.5-5, Post Updated Date:20171116_1451

This Magearna has the TID hacked to be Shiny, nothing changed apart of that.
At the time this post is made, this Pokémon is marked as legal in PKHeX and it is currently unknown if Home can assign a Shiny TID for the Magearna. However, there are no report of a legitimate Shiny Magearna yet and Sword / Shield servers refuse to trade this Pokémon, so i assume it's definitely Shiny Locked.
--EDIT--
This Pokemon is now correctly shown as illegal by PKHeX. HOME will never generate a TID/SID combo with a TSV of 0.
--
The original one is downloadable here:
 

This gift was distributed to commemorate the release of Pokemon Ultra Sun and Ultra Moon, as well as to celebrate Pokemon Movie 20: I Choose You.
This Pikachu was distributed via QR code, similar to how Magearna was given away during the launch of Pokemon Sun & Moon.

It appears that this distribution does not yield any guaranteed IVs.
It's nature is locked to Hardy. Due to a glitch, as long as you don't have the Trainer Shiny Value (TSV) of 1009,
there is a chance of receiving this gift shiny (standard odds, unaffected by shiny charm).
The item Pretty Wing alludes it holding Ash's Rainbow Wing,
as depicted in the Ga-ore card, and the Pokemon TCG card that was distributed as part of the promotion.
The details below refer specifically to this file.
 Species   Pikachu (Partner Cap)   Nickname   (default, in )   OT   Ash   TID   170715   Distribution   In-Game Gift   Location   2017 Pokémon Movie   Dates   (Various)   PID   Not Shiny   Games   All Regions 3DS: UM    Lv. 21                                                                  Nature   Hardy   Ability   Static (1)   Item   Pretty Wing 

Wishing   Moves   (ITALIC means Relearnable)   Thunderbolt   Quick Attack   Thunder   Iron Tail Format Ver.1.0.5-5, Post Updated Date:20171120_0134

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.

At the height of Sword and Shield's narrative, the player encounters an Eternatus.
Eternatus is not capable of the utilizing the Dynamax phenomenon.

   In-Game Encounter  Species   Eternatus   TID   (recipient)   Distribution   In-Game Encounter   Location   on the tower summit   Dates   (any)   PID   Cannot Be Shiny   Games   SWSH   Nature   Random   Ability   Pressure   Item   None                                                               
  Lv. 60       Moves   (ITALIC means Relearnable)   Cross Poison   Dragon Pulse   Flamethrower   Dynamax Cannon

     Lang Slot    OT Name    Nickname   Preset 
Lang   JPN    (recipient)    (default name)    ENG    (recipient)    (default name)    FRE    (recipient)    (default name)    GER    (recipient)    (default name)    ITA    (recipient)    (default name)    SPA    (recipient)    (default name)    KOR    (recipient)    (default name)    CHS    (recipient)    (default name)    CHT    (recipient)    (default name)   Only One Encounter  Format Ver.1.0.8-3b8, Post Updated Date:20191119_1245

This is the first round of Birthday Events for Generation VIII, and it was distributed to players who went to Pokemon Center stores in Japan (thus JP in the title)
during the duration of their birthday month.

Identification would have to be presented upon redemption, and travelers can do so by showing their passport.

Starting February 12, 2020, the JP Birthday distributed as static PID of 06080E2F.
(Before, the PID was random, but unable to be shiny)

   Wonder Card ID #0101: Happy Birthday!  Species   Eevee   TID   191115   Distribution   Serial Code   Location   a Pokémon Center   Dates   Nov 15, '19 to Jan 31, '21   PID   Specified: 06080E2F 
Not Shiny   Games   SWSH   Nature   Docile   Ability   Run Away (1)   Item   None    IVs   EVs HP ALL
RND   ALL
0 ATK DEF S.ATK S.DEF SPE
  Lv. 5       Moves   (ITALIC means Relearnable)   Celebrate   Covet   Helping Hand   Tackle

Birthday Ribbon  Lang
 Slot    Mon's
 Lang    Nickname    OT Name   OT's 
Lang   JPN      (default name)    ポケセン    JPN  ENG      (default name)    ポケセン    JPN  FRE      (default name)    ポケセン    JPN  ITA      (default name)    ポケセン    JPN  GER      (default name)    ポケセン    JPN  SPA      (default name)    ポケセン    JPN  KOR      (default name)    ポケセン    JPN  CHS      (default name)    ポケセン    JPN  CHT      (default name)    ポケセン    JPN Only One Redemption Allowed  Format Ver.2.0.0-11b, Post Updated Date:20201101_2122

This is a wild area event held by Sword and Shield. This event raid allows players to get a chance of Milcery with the Gigantamax icon.
This is the first time, that the Ribbon and Star Sweets were made available. This means that any Alcremie of any flavor and decoration that evolved from this Milcery would be capable of Gigantamaxing.

Coalossal and Flapple were Sword exclusive raids, and Lapras and Appletun were Shield exclusive raids.
Though it is important to note, that the host can invite players of the opposite version to join in the raids.
While the Milcery event was reported to run from January 31st, 2020 to February 16th, 2020,
it was reported the Flapple, Appletun, Coalossal and Lapras will rotate out on February 6th, 2020.
So chances are, this Wild Area Event will run from January 31st, 2020 to February 6th, 2020.
 
To import these files into your save, use PKHeX's block importing function. Our tutorial should guide you through it.
Our first post of this page would contain some data relevant to the importing stage.
There's info and some common questions regarding Wild Area Events here.
To see other Wild Area Events, here.

At the Next Generation World Hobby Fair '20 Winter, players get to experience Max Raid Battles at a "Max Raid Battle Experience Corner".
When a player challenges Gigantamax Coalossal at that corner, they're given a serial code to receive a Gigantamax Coalossal.
When a player challenges Gigantamax Lapras at that corner, they're given a serial code to receive a Gigantamax Lapras.

The official Japanese website claims it is possible to experience it without a Nintendo Switch or the game software. It is unclear if such players would receive a serial code.
This is the list of physical locations (in Japan) and the dates when they were held:
Nagoya Dome - Jan 19 Tokyo - Makuhari Messe International Exhibition Hall - Jan 25 to Jan 26 Fukuoka Yahuoku! Dome - Feb 2 Kyocera Dome Osaka - Feb 9  
   Wonder Card ID #0116: Gigantamax Lapras Gift  Species   Lapras    TID   (recipient)   Distribution   Serial Code   Location   a Pokémon event   Dates   Jan 19 to Feb 29, 2020   PID   Cannot Be Shiny   Games   SWSH   Nature   Random   Ability   Water Absorb (1) or Shell Armor (2) or Hydration (HA)   Item   None    IVs   EVs HP 31   ALL
0 ATK RND   DEF 31   S.ATK 31   S.DEF 31   SPE RND  
  Lv. 50       Moves   (ITALIC means Relearnable)   Surf   Ice Beam   Ancient Power   Bulldoze

Classic Ribbon  Lang
 Slot  Mon's
 Lang  Nickname  OT Name OT's 
Lang   JPN  (default name)  (recipient)  UNSET  ENG  (default name)  (recipient)  UNSET  FRE  (default name)  (recipient)  UNSET  ITA  (default name)  (recipient)  UNSET  GER  (default name)  (recipient)  UNSET  SPA  (default name)  (recipient)  UNSET  KOR  (default name)  (recipient)  UNSET  CHS  (default name)  (recipient)  UNSET  CHT  (default name)  (recipient)  UNSET Only One Redemption Allowed  Format Ver.2.0.0-11b, Post Updated Date:20201105_1939

This gift was distributed to players who purchased Pokémon Sword & Shield via Amazon.
While Amazon US required the dual pack to be order, Amazon JP only required the purchase of either game.
Game must be purchased by Jan 15, 2020 to qualify.
 Wonder Card ID #1606: Clothing Gift   Here's what you got:      Studded Leather Case (Gold)                                   Serial Code | SWSH | Only One Allowed | Nov 15, 2019 to Mar 31, 2020 Format Ver.2.0.0-10b, Post Updated Date:20201027_2342

This gift has been given away on multiple occasions in Europe in the year of 2007 and 2008.
It's likely an internationalization of the Japanese Hadou Mew, which was distributed to commemorate the M08: Lucario and the Mystery of Mew.

In Pokémon X & Y, lies a feature called Friend Safari. It uses the Friend Codes of the Friends on player's 3DS, to allow for some variable encounters.
The encounters in the Friend Safari will have at least two 31 IVs, and also appears to have a higher chance of being shiny.
Additionally, depending on scenario, encountering the Pokémon with Hidden Ability is also possible.

A Friend Safari can have up to 3 encounter slots. The first 2 are guaranteed, however the 3rd slot requires the player's friend to have defeated the Elite 4,
and also be online the same time as the player. (Note: This flag can be activated using PKHeX)

Below is a table of the possible Pokémon found per encounter slot.
 

This gift was distributed to players that attended the Jump Festa '20 via serial code.
This gift was distributed over Jump Festa '20 weekend (December 21st and 22nd, 2019)

   Wonder Card ID #0107: Gigantamax Snorlax Gift  Species   Snorlax    TID   (recipient)   Distribution   Serial Code   Location   a Pokémon event   Dates   Dec 21 '19 to Jan 31 '20   PID   Cannot Be Shiny   Games   SWSH   Nature   Sassy   Ability   Immunity (1) or Thick Fat (2) or Gluttony (HA)   Item   None    IVs   EVs HP 31   ALL
0 ATK 31   DEF 31   S.ATK RND   S.DEF 31   SPE RND  
  Lv. 50       Moves   (ITALIC means Relearnable)   Body Slam   High Horsepower   Brick Break   Bulldoze

Classic Ribbon  Lang
 Slot    Mon's
 Lang    Nickname    OT Name   OT's 
Lang   JPN      (default name)    (recipient)    UNSET  ENG      (default name)    (recipient)    UNSET  FRE      (default name)    (recipient)    UNSET  ITA      (default name)    (recipient)    UNSET  GER      (default name)    (recipient)    UNSET  SPA      (default name)    (recipient)    UNSET  KOR      (default name)    (recipient)    UNSET  CHS      (default name)    (recipient)    UNSET  CHT      (default name)    (recipient)    UNSET Only One Redemption Allowed  Format Ver.2.0.0-11b, Post Updated Date:20201101_2125
Original link: https://www.pokemon.co.jp/info/2019/11/191129_e01.html

This is a wild area event held by Sword and Shield. This event raid allows players to obtain the Gigantamax Snorlax that is not obtainable in the base game.
 
This event allowed some of the previously version exclusive Pokémon be found in the opposing version.
 
To import these files into your save, use PKHeX's block importing function. Our tutorial should guide you through it.
Our first post of this page would contain some data relevant to the importing stage.
There's info and some common questions regarding Wild Area Events here.
To see other Wild Area Events, here.

This gift was distributed to players that are members of the Secret Club, to commemorate the registration of 100,000 members with the Pokémon Secret Club!
In order for players to join the Secret Club, players must pre-order Sword & Shield from a participating Japanese retailer.
Players would then receive a code that is required to register with the Secret Club.

The Trainer ID 000132 appears to be a pun based on Secret Club: 1 (hi from hitotsu - first) 3 (mi from mitsu - third) 2 (tsu; Japanese' roman pronunciation of 2) -> Himitsu (means secret)
Additionally, the words "Club" on the website have been replaced with a Krabby icon; Krabby's Japanese name (クラブ) has the exact same katakana characters as the word Club (クラブ).


 Wonder Card ID #0004: ひみつ's Krabby Gift  Species   Krabby   TID   000132   Distribution   Serial Code   Location   a lovely place   Dates   Oct 04, '19 to Feb 03, '20   PID   Shiny PID   Games   Let's Go Pikachu & Eevee   Nature   Random   Card Per Save   Only One Allowed                                                               
  Lv. 15       Moves   (ITALIC means Relearnable)   Crabhammer   Toxic   Facade   Bubble Beam  Lang
 Slot    OT Name    Nickname   Preset 
Lang   JPN    ひみつ    (default name)    ENG    ひみつ    (default name)    FRE    ひみつ    (default name)    ITA    ひみつ    (default name)    GER    ひみつ    (default name)    SPA    ひみつ    (default name)    KOR    ひみつ    (default name)    CHS    ひみつ    (default name)    CHT    ひみつ    (default name)   Format Ver.1.0.8-3b4, Post Updated Date:20191101_0406
What can be done with these files
PKM creation with PKHeX (drag & drop the wondercard file in the spot where you want the Pokémon) In-Game Mystery Gift redemption with Switch Gift Data Manager

Back in September 25, 2004, the toys retailer TOYS "Я" US in United States had a single day event, where some Pokémon were distributed to players.

These following mons were known to be distributed (red means missing):


Like the MYSTRY Mew distribution, it appears that the distribution across the stores used the same cloned save, and were distributed to players via trade.
Some of the mons in this archive came from LordHuffnPuff.
In this archive, most of the files are .pk3. Also important to note that Machoke & Haunter was received as a Machamp & Gengar respectively, since it was distributed by trade and it wasn't holding an Everstone.
Devolved Machoke & Haunter was added, as it was potentially possible for the player to request for a double trade (to send over an Everstone), and getting the staff to help them attach it to Machoke/Haunter, as unlikely as that may be.

The .pk4 format entries were removed, as they were potentially faked.

This file was hosted on Mystery Gift Servers of Pokemon Omega Ruby, however was ultimately not released for download.
It is speculated that the purpose of this wonder card was simply to test if the serial code service is functioning properly,
as hinted by it's internal name.

This card was uploaded twice on two different occasions, with 2 different internal names.
Both contain the exact same data.

While the distribution title and text is in Japanese, it oddly has the English OT name of Helen.

This Volcanion would be nearly indistinguishable from the Volcanion given out using the used Helen Volcanion wondercard,
provided it was collected on the 3DS of the correct region.

(Though, it'll be illegal to have this Wonder card on your save)

Internal name 1: 588_V_test_EU_E
Internal name 2: 588_Volcanion_EU_EN_Serial_test
 Species   Volcanion   Nickname   (default, save lang)   OT   Helen   TID   10016   Distribution   Intended to be 
Serial Code   Location   a lovely place   Dates   Unreleased as-is   PID   Cannot Be Shiny   Games   EU 3DS: XYORAS    Lv. 70      Nature   Random   Ability   Water Absorb (1)   Item   Assault Vest 
Classic   Moves   (ITALIC means Relearnable)   Steam Eruption   Flamethrower   Hydro Pump   Explosion   WC ID 588: 「ボルケニオン　プレゼント」's receiving text  0x2B Thank you for playing Pokémon! Please pick up your gift from the delivery girl in any Pokémon Center. ボルケニオン　プレゼント ことしの　えいがの　しゅやくポケモン
ばくねつの　ボルケニオンを　プレゼント！
スチームバーストで　ぶっとばせ！

This gift was distributed to players who went to one of the tour locations during the Pokémon 10th Anniversary Journey Across America,
held in the United States back in 2006.

At the height of Sword and Shield's narrative, the player encounters Zamazenta.
Zamazenta is not capable of the utilizing the Dynamax phenomenon.
   In-Game Encounter  Species   Zamazenta
(Crowned Shield)   TID   (recipient)   Distribution   In-Game Encounter   Location   on the tower summit   Dates   When Caught   PID   Cannot Be Shiny   Games   SH   Nature   Random   Ability   Dauntless Shield (1 or 2)   Item   Rusted Shield                                                               
  Lv. 70       Moves   (ITALIC means Relearnable)   Slash   Crunch   Behemoth Bash   Iron Defense

    Lang  Slot    OT Name    Nickname   Preset 
Lang   JPN    (recipient)    (default name)    ENG    (recipient)    (default name)    FRE    (recipient)    (default name)    GER    (recipient)    (default name)    ITA    (recipient)    (default name)    SPA    (recipient)    (default name)    KOR    (recipient)    (default name)    CHS    (recipient)    (default name)    CHT    (recipient)    (default name)   Only One Encounter  Format Ver.1.0.8-3b9, Post Updated Date:20191212_0255

In Pokemon Ultra Moon, after battling Gladion at the base of Mount Lanakila, Lunala can be found at the edge of Mahalo Trail.

After the capture, the player will be given the Lunalium Z by Lillie.
This encounter cannot be shiny. Details below refer specifically to this file.
 Species   Lunala   Nickname   (default, in )   OT   PPorg   TID   171117   Distribution   In-Game Encounter   Location   Mahalo Trail   Dates   Nov 18, 2017   PID   Cannot Be Shiny   Games   Ultra Moon    Lv. 60                                                                  Nature   Bashful   Ability   Shadow Shield (1)   Item   None 
    Moves   (ITALIC means Relearnable)   Moongeist Beam   Cosmic Power   Night Daze   Moonblast Format Ver.1.0.5-5, Post Updated Date:20171122_2158

After being weakened by the grand battle at Megalo Tower, Necrozma returns to Alola.
During this battle, Necrozma can be caught at Mount Lanakila, before the Elite Four.

After the capture, the player will pick-up Ultranecrozium Z, and Colress will appear to give the N-Solarizer and N-Lunarizer Key items.
This encounter cannot be shiny. Details below refer specifically to this file.
 Species   Necrozma   Nickname   (default, in )   OT   PPorg   TID   171117   Distribution   In-Game Encounter   Location   Mount Lanakila   Dates   Nov 18, 2017   PID   Cannot Be Shiny   Games   UM    Lv. 65                                                                  Nature   Adamant   Ability   Prism Armor (1)   Item   Ultranecrozium Z 
    Moves   (ITALIC means Relearnable)   Photon Geyser   Iron Defense   Power Gem   Night Slash Format Ver.1.0.5-5, Post Updated Date:20171115_1724

This Pokémon is a rare variant that is capable of Gigantamaxing, and can only be obtained via Max Raid Battles in the Wild Area.

While always available for capture (if found) in a den in the Wild Area, an event from November 15, 2019 to early January 2020 made it more commonly found in Pokémon Sword, by having it appear in dens normally not associated with it.
To be able to encounter the event variant, user's Switch must be connected to the internet, with the Mystery Gift>Get Wild Area News option used during the event period..
Alternatively user must have connected to the internet and redeemed a Mystery Gift during the event period.