I bought God of War III twice :P

I only bought it again because recently I found the collector's edition in mint condition for a really good price.

i think 50 percent of the games I have bought are repeat buys, games i had as a kid, being lost, stolen, damaged or sold, same for pc games, whenever there's a steam sale i usually end up buying at least 2 games i previously had on disk, just for the convenience of having them all in one place.

Xenogears

Chrono Cross (3 times)

Star Ocean: The 2nd Story (3 times)

Shadow of the Colossus

Zone of the Enders: 2nd Runner (3 times)

Spyro the Dragon

Marvel Vs Capcom 2

Streets of Rage 2

Kartia

The Granstream Saga (I actually don't like the game though)

Spider-Man 2 (3 times)

The Incredible Hulk: Ultimate Destruction

Okami

The King of Fighters 99

Brutal Legend (Didn't like it the first time, but I'll give t another shot)

Hitman 2

Hitman: Blood Money

On the Rain Slick Precipice of Darkness Episode 1

On the Rain Slcik Precipice of Darkness Episode 2

Robotech: Battlcry

Breath of Fire: Dragon Quarter (Two mistakes I'll have to live with forever)

Saiyuki: Journey West

Legend of Dragoon

Jet Moto

Threads of Fate

Destrega

2Xtreme

Fighting Force

Wild Arms 2

Lunar: Silver Star Story Complete

Street Fighter III: Third Strike

Street Fighter Alpha 3

Naruto: Ultimate Ninja Storm 3

Dragon's Dogma (If D21lewis is counting it then so am I)

White Knight Chronicles

Limbo

Far Cry 3

Ico

Kingdom Hearts Re: Chain of Memories

Ratchet and Clank Going Commando

Ratchet and Clank Up Your Arsenal

Uncharted 2

Marvel: Ultimate Alliance 2

X-Men Legends

X-Men Legends 2

Dragon Age: Origins

Deus Ex: Human Revolution

Gunstar Heroes

And A few others I can't remember right now.

Wow Cool Idea OP,
- Metal Gear Solid 2 (PS2), Substance (Xbox), and Legacy (PS3)

I have the 64, GC collector's edition, and 3DS version of Ocarina of Time, and I've played the GC Masterquest edition in its normal and Master Quest modes. I got Wind Waker HD recently even though I played the original twice, and I plan to play this one twice. I bought Metroid Prime Trilogy even though I had the whole trilogy already, and almost bought it again because the first time I got one of those stupid Gamestop boxes with it, and I found it with the box and manual for $50. I was quite tempted, but I resisted. I have the 64 and DS version of Super Mario 64. I got Pokemon Gold and Crystal, the only time I've gotten two versions in the same generation. And believe it or not, I bought Kingdom Hearts: Chain of Memories on GBA and then bought Re:CoM on PS2. If I'd gotten a PS3, I would have bought KH HD 1.5 Remix despite having every game included in it. I still intend to do just that someday. I'll 2.5 remix when it comes out even though I'll have all its games too.

Bought Fallout 3 and NV GOTY editions so I could get all the DLC on a disc.

Also I didn't necessarily "buy" them per say, but I do have the Zelda Collector's Edition and Ocarina of Time bonus discs on the GameCube.

I own most of the old Sonic games in multiple fashions... 

Sonic the Hedgehog - 5 times (Steam, Xbox Live, 3DS VC, Ultimate Genesis Collection, Sonic Mega Collection));

Sonic the Hedgehog 2 - 4 times (Xbox Live, Steam, Sonic Mega Collection, Ultimate Genesis Collection) -  I'd buy this game again if they released it on 3DS VC

Sonic CD - 4 times (Sega PC, Sonic Gems Collection (GC), Xbox Live, and iOS) - I'd buy this game too on 3DS VC.

Sonic 3 - 4 times (Steam, Xbox Live, Sonic Mega Collection, Ultimate Genesis Collection)

Sonic and Knuckles 4 times(Steam, Xbox Live, Sonic Mega Collection,  Ultimate Genesis Collection)

Zelda: Oracle of Ages - 2 times (GBC, 3DC VC)

Super Mario World - 2 times (GBC, Wii U VC)

Zelda: Links Awakening - 3 times(GB, GBC (DX), 3DS VC)

Spyro the Dragon - 2 times (PS1, PSN)

Spyro: Ripto's Rage - 2 times (PS1, PSN)

Spyro:  Year of the Dragon -  2 times (PS1, PSN)

GTA San Andreas - 2 times (PS2, XBL)

The Orange Box (2x 360) - Tbh I bought a second one because I couldn't find my first one... Now I have two.

The Last of Us. Bought the collectors edition(european) and bought the game digitally on the PSN Store.
Final Fantasy X-2. Bought the original japanese, english and the international version. I recently then bought the Resolution box containing the limited edition FFx/X-2 Psvita and X/X-2 remaster. I will soon buy the english version of both X and X-2 for the Vita in march.

Kingdom Hearts II PS2/PS2

Don't ask me why :P

Xenoblade Chronicles...it was so good I HAD to have a 2nd copy just in case. I got it when it had risen to $60 online...and as we all know it has since probably doubled in value from that price. Not that I plan on selling my 2nd copy.

Other games that I've technically bought twice:

Ocarina of Time

Star Fox 64

Super Mario 64

Donkey Kong Country Returns

Super Street Fighter IV

Pokemon

The Sims

The Sims 2

Not sure if VC games count but I've bought a lot of the old Nintendo "classics" more than once.

Oh, and it FEELS like I've bought New Super Mario Bros. four times...because it's basically the same game every time. #lazy