Gameboy Camera, that was some serious fun back in the day

Hmm.

Most Rare:

Zelda: Ocarina of Time w/ Nintendo Power inserts, near-mint, all other pack-in goodies w/ mint box.

Chrono Trigger: near-mint w/ all packins, box, ect.

Ogre Battle 64: Person of Lordly Calibre, near mint w/ all packins, box, ect.

And the same can be said for the rest of my SNES RPG collection:

Secret of Mana
FFIII
Lufia & The Fortress of Doom
Super Mario RPG
Robotrek

And quite a few others.

I also have one of the few still-existing copies of Dragon Warrior (DQ) 3, with orig. manual, and fold-out map w/ weapon and armor charts...But I don't think I have the box.

Oh, and Zelda w/ Gold Cart, but I don't consider that rare when you don't have the box w/ pack-ins.

Nes: Dragon Warrior, Trojan
Snes: Final Fantasy II & III, Secret of Mana, Seiken Densetsu 3 (jap), Secret of Evermore, Might & Magic II,
Mario All Stars, Chrono Trigger,
N64: Ogre Battle 64
Gamecube: Zelda Collection

PS1: Valkyrie Profile (mint), Brigandine (mint), Rhapsody (sealed), Xenogears, Dracula X (jap sealed), Thousand
Arms, Suikoden I & II, Vandal Hearts I & II, Kudelka (jap), Lunar SSSC, Lunar 2, Arc the Lad Collection, Persona,
Ogre Battel LE, Hoshigami,
PS2: Ring of Red, Shadow Hearts, Disgaea, Magna Carta, Stelle Deus (jap), Shadow Hearts 2 (jap),...

I just recently sold Marvel vs. Capcom on ebay for $89. I forgot about Vagrant Story as well, I had it but have no idea what ever happened to it.

Just remembered a few more nes games

Dragon Warrior 1 & 2
Tetris (Tengen)

I usually look for games when I go to swap meets and second hand stores and just recently noticed less and less older games. I kind of hope it's due to people realizing that if you have a great game you enjoy you shouldn't let it go because you never know if you'll ever find it again.

I've got some games others mentioned like Abadox and Tengen Tetris on NES, also have Mario RPG WITH original box/manual.  I"ve kept the boxes and manuals for most of my later SNES games and all of my N64 games so i have a nice collection going there.

Some rare games i have are: Faxanadu w/ original box & manual.

Adventure Island 3 on NES w/ box & manual 

Ys III: Wanderer's from Ys on the SNES just the cartridge.

Uniracers on SNES +box/manual  great game a must for your collection.

Ms Pac-Man and Arkanoid: Doh it Again are both pretty rare late SNES games.

Nights for Saturn, Reboot for PS1, Final Fantasy 7 opened but in mint condition. 

Gold cartriges + boxes for both N64 Zeldas

Conker's BFD and Worms Armageddon for N64... a few years ago my gamestop was offering $25 trade in value for it but i kept it so im guessing it's pretty rare for an N64 game.

Sealed copy of Chrono Chross, though not rare at all now being that u can still buy the game new on Amazon and other online stores, but it'll be worth something down the road.

Suikoden 1 and 2

StarCraft 64 Pal version

Raiden on Playstation 1 Sealed

Mario Tennis, for the Virtual Boy!