It depends, but sometimes Night Trap can sell for a nice chunk of change (at least over $30, not SUPER VALUABLE but still). I have a few different copies of it. Rhapsody can occasionally sell for a shitload (and sometimes not sell for much at all, it's really weird...I've seen it go for $15 and over $100, I don't know what causes that), but my copy is too scratched to really play. Apparently Super Mario RPG can sell for a lot ($70+? I've seen it for that much at least) but I always thought that was one of those games everyone owned and didn't need to buy, still I guess it's more rare than I thought. I have the manual for it too. Illusion of Gaia is rare I think, I can't remember how much it's worth. Wing Commander III for the 3DO can sell for a good amount too, but unfortunately I only have two of the discs because my dad picked them up for $1 at a flea market (although for my own playing I can pirate the other discs). I also have the original PSX RPG Maker but I have no idea what it's worth.
Chrono Trigger (with the box and manual)
Paper Mario
Bushido Blade
Bushido Blade 2
Gunstar Heroes (probably not rare but I've only ever seen one copy of this game)
and then some of the previously mentioned games:
Illusion of Gaia
Harvest Moon 64
SotN
Actually none of these games are rare (in terms of quantity) it's just that idiots on ebay proclaim
everything under the sun to be rare in order to get an exorbitant price out of it. Shame is, idiots will pay bucco bucks for it. Earthbound had hundreds of thousands of copies circulating but because of cult popularity everyone expects 100+ dollerz for it. I have a small list of ACTUAL RARE GAMES that I don't mind sharing (hay guyz look how big my dick is!)
Resident Evil (the original psx version): Had like, 100,000 copies made then was discontinued until the Director's Cut came out.
Ardy Lightfoot: Seriously, this game had about a 50,000 copy run.
Psychonauts: It usually goes for a decent price on ebay but there only 100,000 or so copies made for the ps2 and xbox COMBINED
Wing Commander: Kilrathi Saga - A limited edition collection of the original 3 wing commander games
Shin Megami Tensei: Nocturne - I think it was quoted somewhere that the European "Lucifer's Call" had a larger circulation than the American edition
Elemental Gearbolt: Assassin's Case - a prize given away at convention tournaments. There's like... 50 in existence.
Arc the Lad Collection - Released right before Working Designs went under and had less copies than Lunar 1 and 2
A couple of rare games that I wouldn't mind owning:
Star Fox promotion edition
Donkey Kong gameshow edition (something like that)
Christmas NiGHTS (a limited edition demo disc with a christmas theme)
Team Buddies - I played a demo and it was like fucking LEGO WARS or something. Apparently it had less than 100,000 copies made but it's so fucking cheap online because people are dumb.
Fox Hunt -I'll buy it eventually. I loved the dumb humor in this game and it's ultra rare but so unpopular it goes for like... 2 bux online.
Popful Mail -another rare game but since it's on a system no one cares for it's pretty cheap
Dirty Dwarves -same as above
Chip and Dale Rescue Rangers
Ugh, that's all on the top of my head. I have more lying around because I'm an avid collector but Family Guy is on.