Dr. Brain: Action Reaction was pretty good. Now, I don't know why, for the life of me, the old gray-haired Dr. Brain of Sierra fame became a young red-haired hot-shot in games by Knowledge Adventure, but I can excuse that because this game is actually pretty damn good. It uses the first iteration of UnrealEngine, so you can guess around where the graphics quality is... It did a pretty good job with it, though.
Anyway, the game is, in effect, a first-person puzzler. I mean, sure, you've got a gun and there are guards to shoot, but you can only stun them, and you only get the one weapon. As of such, emphasis is less on combat, and instead figuring out what the heck you're supposed to do to get out of a level. There are plenty of puzzles: things like pipes that drop and corral colored balls (you have to alter the path of the ball to get to the correct bin - harder than it sounds, since these pipe mazes are HUGE), or navigating droids into specific places while keeping others out of those areas, or heck, just getting from Point A to Point B, usually with platforming and guards abound. Plus, I believe you can skip a level, if it's too hard for you, or you're being intimidated by the unkillable (but, as I said, stunnable) hulking guards who always seem to know where you are once they've spotted you in the first place.
Other than that... I dunno, Trackmania's good. Earthworm Jim 3D for the PC and N64 is okay, but those boss fights suck. Glover for the PC, N64 and PS1 was pretty inventive, but the game's really, really hard (a lot of design flaws, methinks - did you know that bowling balls are completely shattered if you lightly place them on spikes? Yeah, me neither). Half-Life isn't obscure in the slightest bit...
Ooh, here's one. Star Wars Droidworks. It's an edutainment title, more or less, but beyond that, you get to make robots and control them to solve various fun little puzzles. I tend to skip the Physics lessons and solve the game instead. I haven't done much with the main missions - the ones where you actually have enemy droids actively killing you - but the training missions seem to be the majority of the game anyway, and do a very respectible job of remaining fun, even if your droid runs on treads and therefore can't jump.
Back to obscure... I own Psychonauts, but I've yet to play it. Rolo to the Rescue was a fun little Genesis game... hard as hell, though. Clockwork Knight for the Saturn wasn't too great, but Clockwork Knight 2 was. Et cetera, et cetera...