Fang of The Sun Dougram - Even among old-school Mecha fans, it's obscure. Yet this is easily one of the most complex and interesting realistic mecha stories I've seen, right up there with Gundam. Too bad its animation quality is so bad, even for a show of its age.
Giant Robo: The Day The Earth Stood Still - Best Super Robot show I've seen (well, after GaoGaiGar and Gurren Lagann), but every seems to pass it off due to its generic name and Old-old-school character designs.
Kaiba - The most obscure show I know, It's actually pretty hard to find fansubs of. It's best and most deep surreal sci-fi/fantasy I've ever seen. I actually had fun trying to figure it all out, and it was enjoyable enough as is, though it was also rather needlessly disturbing at times.
Also, I quite liked LoGH, but because of its currently questionable obscurity status (it was one of the first shows I had heard of when I got into anime, and was one of the first shows I torrented), so I won't put it down just yet.
Iria The Animation - It's freakin' gorgeous, and I found it to be a very fun show overall, though I can't say the plot was that memorable.
Genmu Seki Leada - Okay, most people in Japan know this for being the first OVA, but I doubt many americans have actually seen it. I have. It's a fun watch, though I can't remember much about the story since I had to watch half of it in Japanese, but it didn't lose me, so I guess it was unnecessary.
Idol Project - It's one of the few comedy anime that made me laugh, so it deserves a mention just for that.