Well, this discussion has finally convinced me to stop lurking and make a flippin' account, mostly because just about everyone in this thread has gotten "obscure" mixed up with "not recent". Psi-Ops? CTR? Starfox 64? These are all games that were well-known and well-sold at launch, with the possible exception of Psi-Ops which was outsold only by Second Sight. Phantom Crash (mentioned earlier) was so popular it had a cross-platform sequel, S.L.A.I., and Parasite Eve is a Squaresoft game and is therefore exempt from obscurity because half a billion Square fanboys ranted about it when it was new, and I laugh at the notion that TOMBI and Oni could ever be considered obscure.
With that in mind, I thought I'd stroll in here and blow everyone's socks off with some TRULY obscure titles. Watch and learn, kiddies.
"Wtf is this?" you say? "Starflight is the father of the space trading sim" you say? Well yes. Yes it is. But its Sega Genesis port is surprisingly unknown, which is a shame because it's much more accessible than its DOS grandpappy.
[img src="http://ecx.images-amazon.com/images/I/3199F28336L._SL500_AA197_.jpg"]
Another space trader that went unknown, conceived as Starflight 3 except the developer couldn't get the rights to the name.
[img src="http://homeoftheunderdogs.net/games/n/noctis/noctis.jpg"]
This is Noctis, a freeware procedurally-generated space exploration game. There's a chance you might have heard of it, it gathered a lot of popularity a few years ago when it was featured on Home of the Underdogs. Big selling point here is the procedurally-generated galaxy, large enough to put William Shatner's ego to shame. Between everybody playing over the last several years, only something like 2% of it has been explored and charted.
[img src="http://www.adeptsoftware.com/jetpack/game4.gif"]
It's an indie-developed 2D platformer from the mid 90's. And it's awesome. You don't get much more obscure than this.
[img src="http://upload.wikimedia.org/wikipedia/en/9/98/Hardwar_Coverart.png"]
I'll give a cookie to anyone who actually owns a copy of this. Half a cookie to anyone who'd even heard of it before today.
[img src="http://homeoftheunderdogs.net/games/r/rama/rama-c.jpg"][img src="http://homeoftheunderdogs.net/games/r/rama/rama.jpg"]
Another relatively unknown title from the days of Sierra's adventure games. RAMA was very much a niche title, because few who read the works of Arthur C. Clarke also enjoyed playing adventure games (apparently).
[img src="http://homeoftheunderdogs.net/games/r/retring/retring-c.jpg"]
Same problem, except replace "Arthuc C. Clarke" with "Larry Niven".
[img src="http://homeoftheunderdogs.net/games/a/allegiance/allegiance-c.jpg"]
Maybe not so obscure, but noteworthy in that it's a Microsoft game that went open-source.
And that, ladies and gents, is what "obscure game" means. I've got dozens more if need be.