I really don't have many "rare" games per say. I would like to get some though
Growlanser Generations I guess? I also have a lot of SNES games, but I'm pretty sure most have been rereleased in some digital format.
Scratch that, I have Mega Man Legends 1 and 2.. These games seem to be having trouble being rereleased in digital format due to the voice actors' contracts or something.
Own a bunch of very shitty, old games that could be "rare" because non remembers them and/or bought them.
As far as "very good game that not enough people owned" id say it might be the Original LOTR BFME, those 2 games up to this day sold way fewer copies than they deserved to. I can think of more than 5 strategy games that could even be considered better than those.
Don't think I own any really rare games but here's some stuff I got that's worth a bit on ebay:
Radiant Silvergun, Guardian Heroes, Shining the Holy Ark, Three dirty Dwarves for Saturn
Bare Knuckle III, MUSHA, Elemental Master, Probotector for Genesis
Terranigma, Earthbound, SMRPG, Pocky and Rocky for SNES
Radiant Historia, 999, SMT: Strange Journey, The Dark Spire for DS
Rule of Rose, Shadow Hearts series, Project Zero series, Suikoden III, IV, V, ICO and SotC, God Hand and Okami for PS2
Xenogears, Castlevania SotN, Suikoden I & II, Einhander, Chrono Cross for PS1
Shenmue II for DC