Wow, my first post! Woooo!
The rarest game that I own, by far, is Phantasy Star Online: Episode I & II Plus for the Nintendo Gamecube. I bought it when it was first released for about $30, and I mostly keep my Gamecube around so that I can pop it in every now and then. I think it currently goes for between $60 - $80 online, if it's complete with its case and manual. I'm proud to say that mine is!
I alsp have Phantasy Star II for the Sega Genesis, complete with the original case, manual, maps, and hint book. I feel like that game might be worth more than the PSO set for the Gamecube, but it doesn't matter - neither are for sale, and neither ever will be!
I only own about 40 games across 5 systems (Genesis, SNES, Saturn, N64 and Gamecube) but I love them all dearly. One of these days, I'll find a modestly-priced Panzer Dragoon Saga to add to the collection, but I'm in no rush. Of course, once I pick that up, it'll be the rarest game in my collection, by far!
This is a great thread! I hope people keep chiming in :-D