Video Games:

Gameboy:

Pokemon Red
Pokémon Blue
Pokémon Green(Japan only)
Pokémon Yellow



Gameboy Color:

Pokémon Gold (can also be played on the original Gameboy)
Pokémon Silver (can also be played on the original Gameboy)
Pokemon Crystal
Pokemon Pinball (can also be played on the original Gameboy)
Pokemon Puzzle Challenge
Pokemon Trading Card Game (can also be played on the original Gameboy)
Pokémon Card GB2: Here Comes Team GR!(Japan only)
Pokémon Picross(never released)



Nintendo 64:

Pokemon Snap
Super Smash Brothers (Pokémon appears here playable and non playable)
Pokemon Puzzle League
Pokemon Stadium 1
Pokémon stadium 2
HEY YOU, Pikachu



Gameboy Advance:

Pokémon Ruby
Pokémon Sapphire
Pokémon Emerald
Pokémon LeafGreen
Pokémon FireRed
Pokémon Pinball Ruby & Sapphire
Pokémon Mystery Dungeon Red Rescue Team



GameCube:

Super Smash Brothers Melee (Pokémon appear here playable and non playable)
Pokemon Colosseum
Pokemon XD: Gale of Darkness
Pokémon Box Ruby & Sapphire
Pokémon Channel (with special gift in Europe and Australia)



Nintendo DS:
Pokémon Diamond
Pokémon Pearl
Pokémon Platinum
Pokémon Mystery Dungeon Blue Rescue Team
Pokémon Mystery Dungeon Explorer of Time
Pokémon Mystery Dungeon Explorer of Darkness
Pokémon Mystery Dungeon Explorer of Sky
Pokémon Ranger
Pokémon Ranger Shadows of Almia
Pokémon Dash
Pokémon Trozei
Pokémon HeartGold
Pokémon SoulSilver
Pokémon Ranger Guardian signs
Pokémon Black
Pokémon White
Pokémon Conquest
Pokémon Black2
Pokémon White2



Wii:

Pokemon Battle Revolution
Super Smash Brothers Brawl (Pokémon appears here playable and non playable)
My Pokemon Ranch (wiiwere)
Pokemon Rumble (wiiware)
PokéPark Wii: Pikachu's Great Adventure
Pokémon Mystery Dungeon: Keep Going! Blazing Adventure Squad! (wiiwere Japan only)
Pokémon Mystery Dungeon: Let's Go! Stormy Adventure Squad! (wiiwere Japan only)
Pokémon Mystery Dungeon: Go For It! Light Adventure Squad! (wiiwere Japan only)
Poképark 2: Wonders beyond



3DS

Pokédex 3D
Super Pokémon rumble(Pokémon rumble blast is same game just renamed in USA)
Pokédex 3D pro
Pokemon AR searcher/dream radar
Pokémon X
Pokémon Y



Other games:

Pokémon Pikachu
Pokémon Pikachu 2
Pokéwalker (you get one with HeartGold & SoulSilver)
Cyber Poké Ball
Cyber Pokédex



Pokémon Mini games:

Pokémon Party Mini
Pokémon Pinball Mini
Pokémon Puzzle Collection
Pokémon Zany Cards
Pokémon Tetris (only in Japan)
Pokémon Race
Pokémon Puzzle Collection 2
Pokémon Breeder
Togepi's Adventure
Pichu Bros. Mini
Snorlax's Snacktime



Pics are borrowed from http://bulbapedia.bulbagarden.net/wiki/Main_Page

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Poke'mon Lovers Forever!