Strife - an old Doom engine FPS that had some nice RPG elements and a mission structure that involved exploring and talking to people in a central hub/town area.
Can't think of any. I mean, there are some games I love that were "small" and never super popular/big in the news, but most of the time, games I love that are almost never discussed is, at this point, largely because the game is so old (in gaming terms) that it's just no longer a relevant topic of conversation.
None that I can think of, there's always a bunch people who know of every unpopular game that comes to mind. I think two of the least well known games that I play fairly regularly are Vampire: The Masquerade - Redemption and X-Men Legends 2: Rise of Apocalypse.