I would say the Bloodlines was underrated, yeah. Company died, after all. Later it became sort of a cult classic, but even now, nearly the entire console population and plenty of people I've played WoW with, for example, remain unaware of it. Saddens me that outside my kids, thousand of new gamers will never get to really -relish- the Ocean House. If yo check top whatever lists by IGN, for example, you won't see Bloodlines.
Clive Barker's Undying also, even smaller audience.
I liked Omikron: Nomad Soul a lot. Deeply flawed, but also so ahead of it's time.
If we weren't on these forums, I'd say Witcher - it really doesn't receive the praise it deserves for what it accomplished at the time. Post the prettier Witcher 2, interest went up, but it still remains largely unplayed and underappreciated for, to my mind, it's more ambitious story than Witcher 2 or anything else out at the time.
Gothic 1 and 2. Like Bloodlines, the hardcore know of and have played this. Most gamers have not. Too bad. Grim, fun and tight, one of my favourite pair of games.