The scribble cel stuff is nice, but a bit gimmicky.
I'm planning to write a blog entry about what works and what doesn't work in (Remake) Quake. The short version of it is that Quake's visuals are not photo realistic at all; they are very comicky even when you use hires replacement textures (they even bring it out more - Quake's textures look like paintings, not like photographs). Add to that the low poly models and the reliance on brushes to create environments - everything is angular and blocky. It is much more comparable to Team Fortress 2 than Crysis 2.
Realistic water etc. don't work too well in this comicky environment. I was fiddling around with a very pretty wrought iron fence texture today, and ended up dropping it (despite it being pretty) because it didn't fit with everything else. Similar problem with pretty mosaics or colorful floor tiles - it's a total mismatch in the Quake environment.

It would be reasonable to stick to the comicky appearance and make the most of it, like TF2 does.
Angular, simple, geometric, massive, comicky work well in RMQ. Brush-based detail generally looks more appropriate than fancy sprites etc.
I'm not a big fan of Quake's water surface warp, because water simply doesn't do this in real life, but a "pretty water" shader would be even less appropriate. What I would like is reflective water, though - simple reflection, possibly cubemap, nothing too fancy. Staying in the comicky realm and just adding some polish to the comic.