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Team Rocket Meowth This Meowth was distributed at the Pokémon Day event at Mirabilandia.*It is currently unconfirmed whether this Mystery Gift was distributed to other language versions of the games at this event.
Wondercard ID 120 PID Random Games BW B2W2 Type Local Wireless Dates 07.13.2013-07.14.2013 Nickname Meowth Gender Male Level 15 Nature Random Ability Pickup OT ROCKET SID 00000 Location Pokémon Event Ribbon Wishing Ribbon Ball Cherish Ball Held Item Smoke Ball Moves Fury Swipes Sing Nasty Plot Snatch

ROM Editor for Pokémon Mystery Dungeon games. Refer to the tutorial for details:
 

Pokémon sprites extracted using GfxCrunch. This 7z contains everything one needs to create animated sprites. It is not intended for humans, as sprites have not been stitched together yet.

PID 323970584 Nickname COMBEE Gender Female Level 20 Nature Lax Ability Honey Gather OT Hayley SID 54140 Location Route 205 Met At Lv. 5 Ball Poké Ball Held Item Occa Berry Moves Sweet Scent Gust --- ---

Lucario Doll
This Lucario Doll is a decoration item for the player's Secret Base in the Sinnoh Underground. It was marketed as to be distributed to Platinum versions at Pokémon Centers during the Waku Waku Lucario Fair, a special Lucario merchandising event.
Wondercard ID 045 Games Diamond, Pearl & Platinum
Type Local Wireless Dates 05.01.2009-05.31.2009

Not quite 100%, but the story's been completed at least.

Not 100% complete, but it's in the post game

Movie 2011 Crown Raikou (Shinsegae)
Prior to being distributed at screenings, Raikou was distributed at movie theaters and Shinsegae department stores as a promotion for the 13th Pokémon movie. When sent to a Black or White game via the Relocator, any of the three beasts can activate an event to meet, battle and catch Zoroark in Lostlorn Forest.
As far as it seems, there isn't a Shinsegae Suicune.
   Species   Raikou   Nickname   (default, in )   OT   크라운시티   TID   09180   Distribution   Local Wireless   Location   Pokémon Event   Dates   Sep 11 to Oct 24, 2010   PID   Shiny PID   Games   DPPt HGSS                                                                Lv. 30    Nature   Rash   Ability   Pressure (1)   Item   Micle Berry    Moves       Zap Cannon   Aura Sphere   Extreme Speed   Weather Ball

Classic Format Ver.1.0.7-0, Post Updated Date:20190416_1801

Movie 2011 Crown Entei (Shinsegae)
Prior to being distributed at the screenings, Entei was distributed at Shinsegae department stores and E-Mart stores as a promotion for the 13th Pokémon movie. When sent to a Black or White game via the Relocator, any of the three beasts can activate an event to meet, battle and catch Zoroark in Lostlorn Forest.
As far as it seems, there isn't a Shinsegae Suicune.
   Species   Entei   Nickname   (default, in )   OT   크라운시티   TID   10300   Distribution   Local Wireless   Location   Pokémon Event   Dates   Oct 30 to Nov 28, 2010   PID   Shiny PID   Games   DPPt HGSS                                                                Lv. 30    Nature   Adamant   Ability   Pressure (1)   Item   Custap Berry    Moves       Flare Blitz   Howl   Extreme Speed   Crush Claw

Classic Format Ver.1.0.7-0, Post Updated Date:20190416_1803

Movie 2011 Crown Suicune (CGV)
All three shiny Johto beasts were distributed at movie theaters during screenings of the 13th Pokémon Movie. When sent to a Black or White game via the Relocator, any of the three beasts can activate an event to meet, battle and catch Zoroark in Lostlorn Forest.
   Species   Suicune   Nickname   (default, in )   OT   크라운시티   TID   12160   Distribution   Local Wireless   Location   Pokémon Event   Dates   Dec 16, '10 to Jan 19, '11   PID   Shiny PID   Games   DPPt HGSS                                                                Lv. 30    Nature   Relaxed   Ability   Pressure (1)   Item   Rowap Berry    Moves       Sheer Cold   Air Slash   Extreme Speed   Aqua Ring

Classic Format Ver.1.0.7-0, Post Updated Date:20190416_1758

Summer Shiny Dialga
This shiny Dialga was first distributed at Gamestop stores in the US between August 19 to September 19, 2013.
It was later distributed from August 30 to September 12 at retailers in Canada, Latin America, Australia, New Zealand, the UK, France,
Germany, Italy, Spain, Portugal, Belgium, the Netherlands, Switzerland, Austria, Norway, Denmark, and Russia.
It was also distributed at a Pokémon event at Amaroussion Flocafé in Athens, Greece, on October 05 and again at Public stores in Greece from December 09 to December 22.
 
 Species   Dialga   Nickname   (default, save lang)   OT   SUM2013   TID   08193   Distribution   Local Wireless   Location   Lovely place   Dates   (Various)   PID   Shiny PID   Games   BW B2W2    Lv. 100      Nature   Random   Ability   Pressure (1)   Item   None 
Souvenir   Moves       Dragon Pulse   Draco Meteor   Aura Sphere   Roar of Time   WC ID 148: 「A Shiny Dialga for You!」's receiving text  0x44 Playing Pokémon

Files:
0907_v3.0.5 — Windows drivers ndsplus-64-29nov2012.tar.gz — 64-bits statically compiled UPX compressed Linux build - updated to november 29, 2012 ndsplus-32-29nov2012.tar.gz — 32-bits statically compiled UPX compressed Linux build - updated to november 29, 2012 ndsplus-mac.zip — 64-bits Mac build (only libusb statically compiled) ndsplus-64.tar.gz — 64-bits statically compiled Linux build ndsplus-32.tar.gz — 32-bits statically compiled Linux build Sources:
HK EMS's Downloads Page (Windows drivers) Thulinma/ndsplus on GitHub (Linux and Mac drivers)

Rally PokéWalker Course
This Course Map unlocks the Rally PokéWalker Course for HeartGold and SoulSilver games. It was distributed at Pokémon Centers during the dates above.
Wondercard ID 058 Games HGSS Type Local Wireless Dates 01.29.2010-02.28.2010

Amity Meadow PokéWalker Course
This Course Map unlocks the Amity Meadow PokéWalker Course for HeartGold and SoulSilver games.
Wondercard ID ??? Games HGSS Type Local Wireless Dates 03.12.2011-04.17.2011

Amity Meadow PokéWalker Course
This Course Map unlocks the Amity Meadow PokéWalker Course for HeartGold and SoulSilver games. It was distributed at various train stations for the JR East Pokémon Stamp Rally 2010.
Wondercard ID 064 Games HGSS Type Local Wireless Dates 07.24.2010-08.08.2010

Shopping PokéWalker Course
This Course Map unlocks the Shopping PokéWalker Course for HeartGold and SoulSilver games. It was distributed at Pokémon Centers during the dates above.
Wondercard ID 055 Games HGSS Type Local Wireless Dates 11.14.2009-01.11.2010

After bringing 250 Pokémon to the Ranch, the player can trade a Leafeon for Hayley's Phione. The Nature and PID of this Pokémon are variable.
PID 1409147926 Nickname PHIONE Gender Genderless Level 50 Nature Lonely Ability Hydration OT Hayley SID 09248 Location Lovely place Ball Cherish Ball Held Item --- Moves Grass Knot Rain Dance Rest Surf

After bringing 999 Pokémon to the Ranch, the player can trade any egg for Hayley's Mew. The Nature and PID of this Pokémon are variable.
PID 3878117976 Nickname MEW Gender Genderless Level 50 Nature Lonely Ability Synchronize OT Hayley SID 59228 Location Lovely place Met At Lv. 50 Ball Cherish Ball Held Item --- Moves Synthesis Return Hypnosis Teleport

PID 323977539 Nickname PACHIRISU Gender Female Level 10 Nature Naive Ability Pickup OT Hayley SID 18830 Location Route 205 Met At Lv. 9 Ball Poké Ball Held Item Chilan Berry Moves Grass Knot Growl Shock Wave Quick Attack

PID 323975838 Nickname PIKACHU Gender Male Level 20 Nature Jolly Ability Static OT Hayley SID 19840 Location Trophy Garden Met At Lv. 18 Ball Poké Ball Held Item Shuca Berry Moves Grass Knot Thunderbolt Flash Double Team

PID 323975579 Nickname PONYTA Gender Male Level 16 Nature Naughty Ability Flash Fire OT Hayley SID 01123 Location Lovely place Met At Lv. 13 Ball Poké Ball Held Item Passho Berry Moves Take Down Tackle Tail Whip Ember

PID 323975559 Nickname WAILMER Gender Male Level 45 Nature Lax Ability Oblivious OT Hayley SID 27046 Location Route 223 Met At Lv. 30 Ball Poké Ball Held Item Tanga Berry Moves Rest Water Spout Amnesia Ice Beam

PID 323977664 Nickname VULPIX Gender Male Level 30 Nature Naive Ability Flash Fire OT Hayley SID 21150 Location Lovely place Met At Lv. 16 Ball Poké Ball Held Item Fire Stone Moves Energy Ball Confuse Ray Flamethrower Safeguard

Movie 2011 Victini
This Victini was distributed to promote the pair of 14th Pokémon movies along with several other Victini merchandise and game promotions.
The gender of the OT is determined by the gender of the player.
The first distribution was advertised to US players, while the second distribution was advertised to UK players.
 
 Species   Victini   Nickname   (default, save lang)   OT   Movie14   TID   12031   Distribution   Online Wi-Fi   Location   Wi-Fi Gift   Dates   Dec 03, 2011 
to Jun 12, 2012   PID   Cannot Be Shiny   Games   BW    Lv. 50      Nature   Random   Ability   Victory Star (1)   Item   Fire Gem 
Wishing   Moves       V-create   Fusion Flare   Fusion Bolt   Searing Shot   WC ID 32: 「Virtuoso Victini!」's receiving text  0x44 Playing Pokémon

Summer Keldeo This Keldeo was distributed at Gamestop stores in the US and EB Games stores in Canada during the above dates to promote pre-orders of Black 2 and White 2. It was also distributed at GAME and Gamestation stores in the UK from September 1 to October 11 and at EB Games and Target Stores in Australia from September 15 to October 11. If brought to the Moor of Icirrus along with Cobalion, Terrakion, and Virizion, this Keldeo can learn the move Secret Sword. In Black 2 and White 2, it can learn Secret Sword at Pledge Grove and will be in its Resolute Form while it knows it.
Wondercard ID 069 PID Random Games BW Type Local Wireless Dates 08.27.2012-10.06.2012 Nickname Keldeo Gender Genderless Level 15 Nature Random Ability Justified OT SMR2012 SID 00000 Location Lovely place Ribbon Wishing Ribbon Ball Cherish Ball Held Item PP Max Moves Aqua Jet Leer Double Kick BubbleBeam