I have so many games multiple times.
Metal Gear Solid 2 and 3 - Might not count. I bought the PS2 versions of 2 and 3. Then recently I got the HD Collection for PS3 and Snake Eater 3D, but those two were press copies so I didn't actually pay for them.
Sonic Adventure 1 - Dreamcast, GameCube, and PS3 (for review) and I DIDN'T LIKE IT ANY OF THOSE TIMES
Assassin's Creed - The original version and the one that game with Revelations.
Animal Crossing and The Sims Bustin' Out - I don't know where my extra copies of these even came from. There are two of each on my shelf.
Tons of Mega Man games - Mega Man Anniversary Collection and Virtual Console.
Ocarina of Time - N64, Master Quest GameCube disc, Zelda Collector's Edition GameCube disc, Virtual Console version, and 3DS version.
Spider-Man 2 - I bought it for PS2 then moved and left my PS2 with my parents and bought the GameCube version on a whim for a few bucks.
Genesis Sonic games - Genesis versions, Sonic Mega Collection on GameCube, Sonic's Ultimate Genesis Collection.
Final Fantasy VI - Virtual Console and titty Anthology.
Final Fantasy IV - GBA and titty Chronicles.
Chrono Trigger - Virtual Console and titty Chronicles.
Zelda 1 and 2 - NES cartridges, Zelda Collector's Edition, and 3DS Ambassador Program games.
Kirby's Adventure - Virtual Console, NES, and 3D Classics.
Link to the Past - SNES, GBA, and Virtual Console.
Comix Zone, Dynamite Headdy and Columns - Genesis cart, Ultimate Genesis Collection, Virtual Console
Super Mario 64 - Virtual Console, N64, and DS
Majora's Mask - N64, Virtual Console, Zelda Collector's Edition (and hopefully 3DS someday)
Mario Kart 64 and Paper Mario - Virtual Console, N64
Rayman 3 - GameCube, then HD version (another one that was a review copy though)
Donkey Kong '94, Super Mario Land 1 and 2, Link's Awakening, Alleyway, Kirby's Dream Land - Game Boy, Virtual Console. (In the case of Link's Awakening, both the original and DX versions as physical carts and the DX version on Virtual Console.)
There's a bunch more, too.