#1: For world texture transparency, turning a brush into a func_wall and setting an "alpha" key to a value between 0 and 1 (like 0.5) is a decent method for singleplayer. Qrack does it, Fitzquake mark V does it (but does external tga with an alpha mask poorly, at least in poor lighting). Darkplaces does it (but Darkplaces supports every method well). Quakespasm does it.
EDIT: It seemed all clients disabled transparency when playing online (I assumed just in deathmatch). But I discovered the proquake server tells me that 'alpha' is not a field. So then it seemed that the answer for online transparency is to either hack the proquake server or maybe add "alpha" to defs.qc ? EDIT 2: Adding .alpha to defs.qc is not enough if you're using proquake

One answer is (probably) to use protocol 666: https://quakewiki.org/wiki/Fitzquake_Protocol
ANSWER: For online play, if you can't/won't use protocol 666, the answer seems to be having a texture name preceded by an opening curly brace, like {texturename , and an *external* texture like (texturename.tga in modname/textures. The external texture will have an alpha channel (Layer->Transparency->Add alpha channel in GIMP). It may not matter if the .wad texture has a color 255 transparency, or that the palette's 255 color may be set to whatever your desired transparent color would be. I'm not sure because I've tried so many things at this point, but the external texture and the curly-brace naming are key. For the record, the surface in question is still a func_wall, though the alpha key has been deleted.
The nice thing about the func_wall and external tga methods is, if your engine doesn't support them, you won't have some ugly pink alpha mask pixels. My image is mostly black, and with the func_wall method, the black is mostly/totally transparent. In Proquake it's solid black, of course, but that's far better than that ugly color 255 "pink".
I assume you could change the palette to make black (or whatever) the transparent color, and maybe I'll still do that. But if you're looking for a universal transparent wall texture solution, the external {texture method seems to be the way to go. Just don't use an alpha value plus another method for Quakespasm, or you'll get full invisibility of the texture.
keywords: fence, grate, see-through, glass, Quake 1 level design, Q1, Quake One
Research links:
http://quakeone.com/forums/quake-help/s ... glass.html
http://www.celephais.net/board/view_thr ... 9&end=1183
http://www.celephais.net/board/view_thr ... 66&end=190
http://www.celephais.net/board/view_thread.php?id=37925