Rarest Game You Own(ed)
Sudz
Independent reviews since 1999.
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"Waterworld" (Virtual Boy): the game that cost me the most ($85+ with shipping from the UK) and has given me the least amount of gaming fun. Strictly a conversation piece with friends since none of them will stick their face into the VB for fear they'll go blind... true story! 
"Lucienne's Quest" (3DO): the only traditional Japanese RPG released for the 3DO in the States. Sold it complete in its big box packaging (which I kept when I bought the game from EB in '96) for $135 on eBay two years ago and don't miss it because, unlike other systems, making a back-up copy of the 3DO CD-ROM was easy and I can play the game again if I feel like it. I really miss owning the big box of the game though!
"Panzer Dragoon Saga/Burning Rangers/Shining Force III/House of the Dead/Magic Knight Rayearth" (Sega Saturn): Sega's limited line-up of domestic games released for the Saturn in early 1998 (almost two years before the Dreamcast was released) has gone on to become collector's items, particularly "Saga" and its obscenely low 5,000 copy run. I bought all of these for $39.99 each brand-new back in '98, and been tempted to sell them all (as a group or individually) every time I'm pressed for money or reminded that I haven't played some of them in years.
"Sega Rally Netlink/Virtual On Netlink" (Sega Saturn): only five games were released that could be played online in the Sega Saturn Netlink: Daytona CCE Netlink, Duke Nukem 3D, Bomberman and the two listed above. Except for the widely-available "Duke Nukem" all other games are somewhat scarce, with the Netlink "Daytona CCE" particularly hard to find.
"Tetris Plus/Die Hard Arcade/WipeOut XL (import)/Christmas NiGHTS/Bust-a-Move 3/Worms/Megaman 8/Megaman X4" (Sega Saturn): for some reason or another (i.e. low supply and high demand) these Saturn games command a good price whenever they sell.
"Ogre Battle 64/The Legend of Zelda: Ocarina of Time" Gold Cartridge/Packaging (Nintendo 64): the only rarities I own for Nintendo's workhorse system for the 1990's.
"D/Terry Pratchett's Discworld/Silverload/X-Com: UFO Defense" (PlayStation): little did people know in 1995 that those boxy PS1 games released early in the system's life would be worth so much for collector's a decade later. Each of these games is rare-enough to command an above-average price on eBay except for "Silverload" (a point-and-click graphic adventure set in a horror-themed Western town) which is extremely rare but doesn't really command that much of a price premium.
Final Fantasy Origins/FF Anthology/FF Chronicles (PlayStation): except for the recently-released "missing" FF game on the DS this is the complete collection of Square's NES/SNES RPG series in CD-ROM with cinematics. All with original black labels (not the "green" one's). Something to entertain me when I retire in... oh, 25-30 years! 
Disney Golf/World of Outlaws: Sprint Cars/Firefighter F.D. 18/Rez/Zone of the Enders: 2nd Runner (PlayStation 2): self-explanatory.
Other rare games I've owned that I've unloaded on eBay (and regreted doing so almost immediately because of their rarity) include "Dragon Force" (Saturn), "Chrono Trigger" (SNES), "Super Mario RPG" (SNES), "Final Fantasy III" (USA Version, SNES), "The Raiden Project" (PS1), "Dance Dance Revolution: Disney Mix" (PS1), "Herc's Adventure" (PS1) and "Return Fire" (PS1).
Here in the UK WipEout XL on the Saturn is dirt cheap, Christmas Nights too.
Is the gold cartridge Ocarina of Time considered rare? I wasn't even aware it came in other colors; that is the only one I've ever owned.
The gold Zelda and the black Turok 2 are not rare.
[QUOTE=bluemonkey]The gold Zelda and the black Turok 2 are not rare.[/QUOTE]
I meant to say "Zelda" Gold cartridge AND package in mint condition. "Turok 2"?