Many verisons of 1 game

ToxBox

Power Star
I have Kirby Adventure NES, I have many remakes of this game,
Kirby Adventure NES, getting it tomorrow, real copy
^ on Wii Virtual Console
^ as 3D classic on 3DS
^ GBA remake, Nightmare on Dreamland
 
I own Mario Bros. four times over. Once in Super Mario Advance(I also own Super Mario Bros. 2 on Virtual Console, so there's another one), once in Super Mario Advance 3, once in Animal Crossing, once on Virtual Console. I own Donkey Kong, Excitebike, Wario's Woods, and technically Super Mario Bros. and The Legend of Zelda on both Animal Crossing and Virtual Console. That said, I am not actually in posession of any of the aforementioned NES games in my house in Animal Crossing. I only have Donkey Kong Jr. Math and Balloon Fight.

I own Sonic Spinball, Sonic the Hedgehog 2, Sonic Triple Trouble. Sonic Drift 2 , Tails' Skypatrol, Tails Adventure(all Game Gear titles) in both Sonic Adventure DX and Sonic Gems Collection. I have the Genesis versions of all those and more in Sonic Gems Collection of course but if I remember correctly all SEGA's 8-bit ports of 16-bit games were pretty different. I also own Ristar both in Sonic Gems Collection and on Virtual Console.

So, mostly thanks to games that pack-in their predecessors as minigames, I have plenty of these.
 
Nintendo and Square Enix are masters of remakes and ports.

I've got Zelda: Ocarina of Time on my N64, Gamecube, Wii, and 3DS (x2).
Also: Super Mario 64 on my N64, Wii, and DS.
Not to forget: Lylat Wars on my N64, Wii, and 3DS.
 
I own the original Metroid 4 times over.
- original cart
- unlocked it in Metroid Prime
- unlocked it in Metroid: Zero Mission
- downloaded it for free via the 3DS Ambassador Program

I own Mega Man 1-8 twice over thanks to the Anniversary Collection.
I own Mega Man X 1-6 twice over thanks to the collection disc.
Mortal Kombat 2 twice over thanks to Midway Arcade Treasures 2.
 
Games I have at least two copies of:

The Legend of Zelda: Ocarina of Time
-Original N64 version
-3DS version
-On The Legend of Zelda: Collector's Edition

Donkey Kong Country
-Original Super NES version
-GBA version

Star Fox 64
-Original N64 version
-3DS version

Super Mario 64
-Original N64 version x2
-DS version

Sonic the Hedgehog 1
-Original Genesis version
-Sonic Mega Collection
-Sonic Mega Collection Plus
-Sonic's Ultimate Genesis Collection

Sonic the Hedgehog 2

see above

Sonic & Knuckles

see above

Sonic the Hedgehog 3

^

Probably more than that.
 
I have Donkey Kong Country on SNES, GBA, and GBC. The other two old DKCs I have on both SNES and GBA.

I also have two copies of Super Mario Land for Gameboy, and a downloaded version on 3DS.
 
I have Super Mario 64 on Wii VC and on DS
I have all 3 Animal Crossings, but idk if that counts.

Sadly, that's it.
 
From what I remember off the top of my head:

Super Mario 64 (N64 and DS)
Donkey Kong '94 (GB and 3DS VC)
VVVVVV (Steam and 3DS)
Cave Story (PC, WiiWare, 3DS)
Metroid (GBA, Metroid Fusion)
Dr. Mario (NES, GBA)
Super Mario Bros. 2 (NES, GBA as Super Mario Advance)

There's probably a few more.
 
I have two copies of Super Mario 64 DS — one is the American version, one is the European version. I also own Super Mario Bros., Super Mario Bros.: The Lost Levels, Super Mario Bros. 3, Super Mario Bros. USA and Mario Bros. twice each.
 
- Super Mario Bros. 3 for NES and Super Mario Advance 4: Super Mario Bros. 3 for GBA
- Super Mario 64 for Wii VC and Super Mario 64 DS for DS
- VVVVVV on Steam and VVVVVV for 3DS
- Half-Life on Steam and Half-Life: Source on Steam (I'm looking to get Half-Life for PlayStation as well)
- Super Mario Bros. for NES and Super Mario Bros. Deluxe for GBC
- 2 copies of John Madden Football '93 for Genesis/Mega Drive (getting rid of one of these soon)
- I once had 2 copies of Pokémon XD: Gale of Darkness for GameCube

That's all I can think of
 
I have :

- Super Mario Bros : The lost levels and Super Mario bros 3 on VC, and Super Mario all stars 25th Anniversary
- Super Mario 64 and Super Mario 64 DS
- Pokemon Red/Blue/Yellow and Pokemon Fire Red /Leaf Green versions
- Pokemon Gold/Silver/Crystal and Pokemon Heartgold
 
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