I like this thread! Lets see what I got for rares:
NES:- Bubble Bobble 2
- Gimmick! (Famicom)
- Little Samson
- Mighty Final Fight
- Panic Restaurant (Complete for $5!)
- Power Blade 2
- Snow Bros (w/ Box)
- Mega Man 9 Press Kit Sealed (Not really an NES game but yah)
SNES:- Captain Commando
- Breath of Fire
- Chrono Trigger
- E.V.O.
- Final Fight 2 & 3
- Illusion of Gaia (Complete)
- Mega Man X 2 & 3
- Secret of Mana
- Sonic Blast Man 2
- Super Adventure Island II
- Super Castlevania IV (Complete)
Master System:- Ninja Gaiden (Complete)
Genesis:- Castlevania Bloodlines (Complete)
- Crusader of Centy (Complete)
- Golden Axe III (Complete)
- Gunsta Heroes
- Moonwalker (Complete)
- Punisher
- Raiden Trad (Complete)
- Splatterhouse 2 & 3 (Complete)
- Streets of Rage Trilogy (Complete)
Turbo Grafx 16:
- Neutopia 1 & 2
- Splatterhouse
N64:- Conker's Bad Fur Day
Dreamcast:- Power Stone (Complete)
PS1:- Legend of Mana (Complete)
- Parasite Eve
- Tales of Phantasia II (Complete)
PS2:- Bloody Roar 4 (Complete)
- Mega Man X7 & 8 (Complete)
360:- Deathsmiles Limited Edition (Sealed)
Virtual Boy:- Mario Clash (Complete)
- Panic Bomber (Complete)
- Red Alarm (Complete)
- Vertical Force (Complete)
- Virtual Boy Wario Land (Complete)
Probably have a bunch more people would consider rare, but I decided to mention what I consider to be the rarest of the bunch.