As Chocobo Kick pointed out before our rarest are probably

Factory sealed Final Fantasy 1 (NES)
Snatcher or both lunars (Sega Cd)
Panzer Dragoon Saga (have an extra gonna put up on ebay soon)
also have Klonoa and DBZ Final Bout for Playstation least till i sell the DBZ
Math Blaster and Pirates Gold complete for Genesis
SOS sealed for SNES also Harvest Moon complete and all the Mega Mans complete

not sure what the rarest one would be overall though.