I dunno how many of these are lesser known but these are a few of the RPG's I really enjoy on the computer, some of them are pretty old now:
Ultima Underworld
Gabriel Knight (I dunno if this is strictly an RPG, great game though)
Arcanum
Wizardry 8
Neverwinter Nights + expansions (especially Hordes of the Underdark) - best D&D based game I've played.
Legends of Lore (old Westwood game pretty hard to get a copy of)
Lords of Magic (Kind of like a combination of Turn Based stratergy, empire builder and a RPG, used to multiplayer it with a mate, takes months to finish)
Vampire The Masquerade: Bloodlines (WoD/VtR is another table top RPG I play, game is really well done)
There's a really good one I can't remember the name off. It was one of the first RPG's I got into when it I played it on our first computer (386) it was made during the cold war and you were a spy inside the USSR, I think it was made by Microprose, gah I've probably still got it on a 5.4' disk at my parents house, it was really good...
There's another one where you were a hacker was kind of Cyber punkish pretty old too gah all these old games I've forgotten about
Wow, someone else who has played RPGs on the computer. Gosh. Welcome to the dinosaurs' club. I had given up hope. Anyway GK was supposed to be a quest, but good call. I heard Jane Jensen (the author, for those who don't know) has went into full-time writing, which I suppose is a good thing. Legends of Lore... You mean Lands of Lore? Westwood, may they rest in peace, did not make that many RPGs/ Anyway, LoL is abandonware by now, iirc, so it should be relatively easy to obtain (search abandonware). Just get Dosbox to run it, and you should be fine.
Arcanum was nice, but I never got very far. Those people had worse maps than Fallout, and Fallout is some 10 years old now. I hope I don't have to list fallout as "lesser known." Seriously... unfulfilled potential, Troika is thy name. Speaking of which, Bloodlines does rock, on so many levels. Just as an indication of how it got some people hooked in spite of early release, some awesome cut content and poor support (Troika went belly-up around version 1.2) the game is zealously updated by fans over 3 years after its release. The game is pure gold, from the NVidia ad in the introduction (starring a certain Toreador) to some of the greatest ingame music since Red Alert. My jaw dropped when I entered the Asylum, and the ending theme (Swamped, by Lacuna Coil iirc) was great. I love those guys. On the topic of Vampire, Redemption was nice in some ways, although it had insane camera control and was sometimes way too reminiscent of the 1st wave of hack and slash games. Nifty dialogue despite the rather cliched angsty knight-turned-vampire bits.
Neverwinter nights is good, especially with some of the fanmods over at NWVault.ign.com, but come on, man, best D&D game? Not by a long shot. Baldur's Gate, especially 2, blows it out of the water imo. It is not exactly "lesser known," at least if one follows CRPGs, but it is practically perfect. Well-made graphic (as beautiful as pre-3D gets), great story and NPCs, good setting, cameos from some legendary characters, it is just great.
Icewind Dale II is a good diamond in the rough, btw - more hack&slash oriented, but with some interesting dialogue for characters of untraditional races. Play it with a drow and watch the elves freak out
Still, if we are to speak of D&D lesser known games, I nominate Planescape: Torment. This is a hands-down incredible RPG. IMO an RPG lives and dies by its story, and in that regard, PS:T is immortal. The graphics can be a bit old, but I can not praise it enough. Words fail me when I have to speak of the game and characters. The NPCs were simply incredible. Morte is hilarious, and only HK-47 even comes close to that. Annah... one badass tiefling, that (NWN 2's Neeshka is a poor rip-off, and should be burned at the stake for defiling Annah's legacy - oh, and shishkebabed with wrist daggers, just to be sure). Dak'kon, Grace, Vhailor... all of these, as well as the rest of the gang, deserve more mention that I have the time to. Seriously, those of you who have not tried Planescape: Torment, do. If you like RPGs, it is a treat for the heart.
So, what else... Lionheart was kinda cool. It makes me wonder if the scriptwriter was on, well, controlled substances when s/he was taking their history lessons, or they just have a wild imagination. Even though some parts were annoying (I hated the "henchmen" you got, they weren't even decent meatshields), it deserves an honorary mention for hilarity. Seriously, just how can you link Jeanne d'Arc and a genie? Finally, of course, the Knights of the Old Republic games are a staple, but I doubt they count as "Lesser known." Right?