Cheater! Quit cheating, you see-thru-water cheater.
Just kidding. Glad to see some validation on the transparent water thing. I use transparent water, and I've had a hard time explaining to some WinQuakers why I don't think it's a cheat. Some people have given me so much grief over it that I've started to wonder if it really is OK.
With GLQuake's r_wateralpha setting and water-vis'd maps you can see through the water surface, but generally you can only see map features like walls, doorways, pillars, etc. You can also see particles, e.g. the red static around a berserker's head or the radiation pain effect. If the server's maps are also water-vis'd (which is pretty rare) then you can see anything -- players, missiles, monsters, weapons, etc -- through the water. That is pretty unfair to non-GL players, but if the server op went to all the trouble to water-vis the maps then it's pretty clearly allowed and expected.
I water-vis'd my maps back when I first got a Voodoo card. I think it looks much better. The opaque water (can't see through, as in WinQuake) was just a hack to make the software renderer go faster, and I really don't think it's how Id intended Quake to look. It's ugly as hell. I occasionally set r_wateralpha to 1 for opaque water and I don't think it really makes a difference in my playing -- I already have the maps so firmly memorized that I don't really need to see where the doorways are to hook them through the water. Consider the "start" map. Stand on the floor above the red armor pool and hook down to the doorway that takes you to the quad -- do you really need to see to be able to hit that doorway with the hook?
Unfortunately some fairly influential people consider transparent water to be cheating. Some match servers (clan ring? clan arena? something like that) force r_wateralpha to 1 when you connect, clearly implying that transparent water is not allowed. If you look in the ProQuake source code you'll see that transparent water is not allowed in "cheat free" mode.
In my opinion modified pak with fullbright models and featureless walls
are cheating. I've never modified or replaced any models in my pak files, so I definitely lose sight of people in dark rooms. I also have a very hard time seeing brown or green players on most maps, which is why I made the IHOC server replace shirt colors 1, 3, 5, and 11 with brighter colors (14 or 15). But I can't really fault people too much for minor pak modifications, because I've water-vis'd my maps and some people consider that improper.
Pak hacks that let you see around corners definitely cross the line. I'll ban anyone I catch using that.