It's hard to say because sometimes you think something's unheard of only to find that it's more popular than you thought. And there's relativity to how underrated something is... but...

Planescape: Torment - This is a weird one because in some ways I think it has more vocal fans now than when it came out in 1999. It won RPG of the Year but didn't sell well; now tons of people are trying to find a copy. Awesome game that should have been marketed better.

The Suikoden Series - Depending on who I'm talking to, it seems like this is either really popular or extremely obscure. At any rate, I'm not a massive JRPG fan, but this is a series I've really enjoyed. In a world where it seems of console RPGs all that anyone seems to talk about is Final Fantasy, Suikoden offers some of the best of that genre while also offering a really unique world and some very cool ideas and wonderful characters.

Shadow Hearts Covenant - Just played this a little while ago and wondering why I seem to be the only person who's heard of it. Another JRPG, but with a very different feel than the others I've played, set in an alternate World War I era Earth with fantasy elements.

I second another poster's mention of Nethack. Good old Roguelikes.

Titan Quest -- This is a fairly recent game, having come out last summer, but didn't get widely marketed. It's very Diablo-like in gameplay, with an "ancient-worlds" setting. It's well-written and paced; the interface is nothing new if you've played Diablo, but it's a well-done game and should get some credit where it's due.