I second the people who said Dark Corners of the Earth, Giants, Majesty, Arcanum, Advent Rising, Undying and VTM Bloodlines. For me, Gothic was the opposite of obscure, it was a formative gaming experience for me and all my friends. I'll add the following:
- Clive Barker's Jericho, which had amazing ideas and characters and ended up a "bowl o' brown"
- Hostile Waters: Antaeus Rising, which was this brilliant strategy game that had you using a very limited number of units to achieve difficult goals, what Carrier Command Gaea Mission is trying to riff on now, only without the exciting unit types and strategic depth. It deserved a sequel and more success for its amazing ideas. Also, if there was ever a single player game that screamed for multi, even just tacked on, this is it.
- Rise of Nations: Rise of Legends, which made the franchise fun for me and had this nice story and great factions with amazing art. The implementation of said story was kind of crappy, filler missions having just 2 lines of text assigned to them but still.
- Arx Fatalis, an RPG with incresible freedom a nice, fleshed out world, rats on a stick and an interesting magic system, from the people who gave us Dishonored. If you're going to say it is a legend and not obscure at all, then why hasn't Arkane reaped the rewards it deserved? It's been stuck doing grunt work for other games and Dark Messiah for the better part of ten years.
- Septerra Core - Western JRPG with everything it entails and a nice world.
- Freelancer - still the standard to beat in arcadey space sims with lots of freedom, that dont make you want to blow a gasket because of the controls (like the X series)
- the Legacy of Kain series, a vampire, time travel, still a better love story than twilight platformer and adventure, because of the story and the characters