glquake.exe runs just fine now in 5.0. All you need to do is run it from the command line or with cxrun, and add the following parameters to the command.
glquake.exe -noipx -nojoy -width 1024 -height 768 -bpp 32
The non 3d accelerated version (winquake.exe) still does not run at this time. But good news that the GL version does.
Note: you may need to remove the 3dfx minigl driver. Just delete (or rename) the opengl32.dll file in the quake directory.