I have 2 copies of GT5... I had bought one in UK and was waiting for it to deliver for a month, them there was the release event in Brazil close to my home and I got there and needed the game to get an autograph and were dying to play it so I double dip on a game I hadn't opened yet. And Raibow Six HD collection I have 2 (didn't remember I had one that I hadn't played before buying it again and never opening).

If emulators count I have about 4 or 5 collection of all Master System, Mega Drive/Genesis, Nintendo, Super Nintendo and N64 in several computers I have bought and re-downloaded all the roms =~]

I only bought 1 game twice and that's Fallout 3.
I'll probably be getting GTA V and TLOU:R when they drop in price for ps4

Oh man.

Ff7-9 psn/ps1
Ff1 way to many times
Persona 3 psp/ps2/ps2
Ffx ps2/ps3/vita
Suikoden psn/ps1
Chrono cross psn/psn
Baulders gate pc/pc
Persona 4 vita/ps2

Tales of symphonia gc/ps3

Atelier rorona/meruru/totori ps3/vita
And many others

Honestly, there aren't that many. Since I had a launch PS3, I had BC so I didn't need to rebuy anything I absolutely had to play from previous gens. The only games that come to mind are GTAIV (bought the CE on PS3 originally, then built a gaming rig and bought it for PC...pretty much ignored the PS version after that), and Doom 2, because the floppy disks got all fudged up after I loaned them to a friend.

The rest of my games, I just take obsessive care of, so they don't get scratched, broken etc...  they all have their jewel cases, and are always put back when I changed to a different game.

Ocarina of Time (Wii VC / 3DS)
Super Mario 64 (Wii VC / DS)
Super Mario Bros. 3 (Wii VC / GBA) soon to be Wii U VC too if only there were cross buy for 3DS or at least a heavy discount.

Those are remakes though, if we say completely similar to the original then it is

Super Metroid Wii VC / Wii U VC (for a very small price though)
FF7 (PS1 / PS Store)
Super Mario Bros. (Wii VC / Wii U VC)
Super Mario Bros. 2 (Wii VC / Wii U VC)

I can't remember anything else atm.

So many...

Marvel Vs. Capcom 2... Dreamcast, PS2 (X2), PS3 (X4) once digial for myself, another digital for a friend and I have the limited edition collectors PS3 case, which code no longer works because capcom lost the marvel vs. capcom license. and bought it for another friend who didn't actually like the game, wtf...
Tekken Tag Tournament 2, PS3, disc and digital
Tekken 5 PS2 (X2) PSP, PS3. (psp and PS3 version are Dark Resurrection)
Soul Calibur II, PS2, PS3
Mortal Kombat (PS3, PC) pc version's complete edition was on sale for 5 bucks.

There are others... they dont count because they were stolen and i replaced them.

Hitman Blood Money. I have two copies on PS2 and the digital one from the HD Collection on the PS3.

Hitman Contracts. PS2 and HD Collection on the PS3.

Resident Evil 4. Two copies on PS2. First copy got lost somewhere and I was like crazy looking for it. So I re-bought it.

Oh yeah, I bought FFVII twice, still have 8 and 9 kicking around somewhere though.

There are a few actually:

Metal Gear Solid 2 (PS2) / HD rerelease (PS3)
Metal Gear Solid 3 (PS2) / HD rerelease (PS3)

Ocarina of Time (N64) / Virtual Console (Wii) / remake (3ds)
Majora's Mask (N64) / Virtual Console (Wii)

All sorts of different Pokemon versions, that are essentially the same game; (Red, Yellow; / Diamond, Pearl, Platin;)

None.