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.