A few (some mentioned above) that I wouldn't consider obscure, but that you might not have heard of:
Space Opera - When this was published, FGU was a major force in small-company roleplaying. (Yes, I know that's contradictory.

FGU might even be keeping it nominally in print.
Universe - SPI pushed this really hard, and at the time SPI was about as much of a force as White Wolf is now.
Space 1889 - GDW bought lots of ads for this and published a dozen or more supplements two (?) boardgames, and a set of miniatures rules, and RAFM made a miniatures line for it.
DragonQuest - SPI, killed in the bankruptcy/TSR takeover. Some very nice ideas for its time. Heavily advertised.
Borderline obscure:
Tales from the Floating Vagabond - Avalon Hill. One of the best humor RPGs.
Man, Myth, & Magic - Yaquinto brought this out with a fair amount of press. It has some interesting ideas, but the company stopped publishing games soon after it came out.
Bloodshadows - West End Games. Fantasy Noir. Excellent world with decent fiction support.
Blue Planet - Hard SF roleplaying. Well reviewed, and I have a copy, but I've never played it.
Amber Diceless Roleplaying - Phage Press. More interesting ideas, and you can still find people playing this one.
Obscure:
Lace & Steel - Pharos Press (at least the second edition) Mentioned above. Very interesting duelling system.
Legacy - A "second generation, multilevel, role assumption game". Stone age roleplaying that has rules for inventions -- like flint-tipped spears.
Metamorphosis Alpha - TSR. Roleplaying on a generation starship that has fallen into barbarism. Largely based on Robert Heinlein's "Universe". Rapidly superseded by Gamma World.
En Garde - GDW. Fun duelling system. This is a very early game that's only borderline roleplaying.
Timeship - Yaquinto. Have it. Haven't played it.
Furry Pirates - Atlas. Anthropomorphic pirates. Have it. Haven't played it.
Space Quest - Mentioned above, this one was actually pretty good. (And no, I'm not interested in selling.
All categorizations subject to dispute, of course.