Quake III Arena doesn't have this problem! My guess is that Quake II was developed and tested on old video cards and drivers that rendered textures very differently. I've never understood why Quake II is so dark and murky to begin with. (Drivers vary in the level of control they provide, and some old cards don't support gamma correction at all, so I don't see this as a viable solution.) I also have not had much luck with driver-level gamma controls. Fresh installs of the game are way too dark on most systems, and the built-in brightness controls have nasty trade-offs discussed below.
I love Quake II to death and have played it a zillion times, but I've always struggled to get the brightness right. Here's some background on how I discovered this approach. Hope the above guide is useful to other fans of Quake II.
