Ninpanda on 17 February 2011
I don't think SotC and Ico count as "unpopular." Hell, they were even voted to be the 8th and 38th best games of all time on this site, respectively.
Anyways, my favorite obscure-ish games are probably either Zeus: Master of Olympus (A kick-ass city-building game for the PC.) or Spider-Man & Venom: Separation Anxiety. (A kick-ass beat em' up for the SNES.)
