Some time ago i wrote a Quake 1 launcher that could scan my mods and PAKs. You can find it here :-).

You may also want to combine it with Quake Injector which downloads any maps, mods and their dependencies from the excellent Quaddicted site (a repository of every single player map made ever... or close anyway). MiniQL has a button to launch Quake Injector (make sure you also install Java).

EDIT: also forgot, make sure you get Quakespasm (or a similar engine, but personally i use Quakespasm) to replace GLQuake. Most mods these days need an extended engine and do not run in the original GLQuake. In addition Quakespasm fixes several bugs in the original engine, like restoring the lightmap range (the software renderer has a 0-200% light range whereas GLQuake has 0-100%, which makes things a bit dimmer and removes bright areas), adding support for non-power-of-two textures (the original GLQuake scaled down in an ugly way any texture that wasn't a power of two), improving mouse support, adding high 32bit resolutions, etc.

MiniQL is a solid piece of work. Thumbs up. :-)