I got the impression the OP was looking for first-person action-adventure games, or at the very least a 3D one, since Metroid Prime is a first-person action-adventure game. I think these sort of games are mostly on console due to the analog stick. Keyboard doesn't allow for precise movement so developers can forget about incorporating Metroid Prime's platforming for sure.

The Batman: Arkham games have a certain Metroidvania feel to them, even if it's not the main focus of the experience.

I was about to write Powerslave (Exhumed), only to notice that I had the console (PSX and Sega Saturn) versions in mind (the PC version is a linear FPS). The console version is pretty much a precursor for Metroid Prime.

I think that something like Metroid Prime could work on the PC. Samus feels a bit clunky, which is good considering that she is an heavily armored space marine - that can actually fit into keyboard controls. Something like the Morphball would be a bit more questionable, but it can be done via mouse in a way similar to Hamsterball.

Hey, if there are any developers who want to make a Metroid Prime descendent, please kickstarter it. I would pay to have a FPS game that breaks away from killing fields being the prime focus.

Obvious answer: Metroid Prime 2 and 3!

I think I read in a thread that you play an emulator, is that correct? I can vouch for that Metroid Prime 2 is as playable as the first one (I think it crashed a few more times though) but Metroid Prime 3 Corruption is a Wii game and is insanely unstable and requires a i5/i7 dual core at 3.5 to 4.0GHz or so. I did try it though just before the summer, managed to play about 30 minutes without a single crash and the framerates were in the 30 area on my Q9450, 4GB, GTX470 rig.

Ah yes that's exactly what I was thinking but I just couldn't quite put it into words. And you're entitled to your opinion. You don't sound very biased either.

Maybe I should try some more of those games some time.
Funny, 2 is the only one I haven't played. I've recently been wanting to play them all again though. 3 I remember being very very good in every aspect. Only thing anyone could complain about is that it's not very different from the other 2, echoes included, not that this is really a bad thing as each game is original enough in level design, story and such.

Other M on the other hand... THE BABY THE BABY THE BABY!