Oh man they have Kreed! -- that was sucked days of my life away :)

I have a thing for that stye of game... Some other off the wall ones are:

You Are Empty -- a russian horror themed game in the genre of Painkiller
Gunman Chronicles -- based of the half-life engine and had some cool weapon mods with the most memorable game/level design in ages
Exodus: from the earth -- pure cyberpunk thriller FPS based in 2016 :p its a little wacked out and graphically more mature then the rest but it FEELS like a late 90's shooter at its core, bugs and oddities galore but.. that style is so fun :)

These are my cream of the crop but you gotta love this stuff to appreciate them :)

Descent and Descent 2. Those two are fantastic but don't get much attention for whatever reason. Forsaken is also good, but less so.

Malice for Quake. It requires the original Quake to play, and takes some effort to get running properly. Stupid fun, because of the bad voice acting and writing.

On the off chance that you haven't already then Unreal definitely, especially when running in software mode, which I haven't tried on a modern system yet. It's a bit later than Quake (2yrs) though, but to me it also has that early 3D graphics vibe.

Unreal is one of my favorite games of all time :)

Can it be Steam? Cell Shaded? Indie? Recent? If so, check out Wrack.

Or for something uglier, Bedlam.