Mine aren't really that obscure, but these are the ones I like that nobody I come across usually knows:
Splashdown
Supreme Beings of Leisure
Casey Stratton
Devin Townsend
The Divine Comedy
Splashdown is my favorite of all these. They were an electropop/rock band with a quirky-cute lead songstress. They recorded and played live in the late 90's but didn't sell many records. I recall rumors of a massive label dispute. I collected all their music after I heard Karma Slave from the Titan A.E. Soundtrack. They split up and now do solo projects (i.e. Universal Hall Pass, Symbion Project) that are sometimes fun, but don't scratch the same itch.
I know Devin isn't that obscure, but for some reason I haven't met anyone (i.e. face to face) in years who has heard of him. He's done voices on Metalocalypse, so someone else out there has to be listening to his albums.
Also, I liked a band for awhile called Groovelily after I saw them live, but I've found their actual records to be a little dull. They feature a lot of electric violin, and the instrument isn't nearly as cool on record as it is in person. I have yet to run into someone who has heard of them.