Here a list of GLQuake commands (From www.quakehole.com) 1-22-97:

Press the ` key to access the command line interface then for
Transparent Water type:

r_wateralpha 0.4    (or any number 0-1) (1 is default)
r_novis 1    (needed for transparent water until the new VIS util is released)
released)    (0 is default)

note: It will run amazingly slow with the r_novis command, this is just
a workaround so you can see the effect.. to actually run a map with
transparent water at a reasonable speed you need a map which has been
VIS'd with the new VIS util that is not yet released.

Shadows:

r_shadows 1 (0 is default)

Mirrors:

r_mirroralpha 0.3 (or any number 0-1) (1 is default)

Other Commands:

gl_polyblend 0 (turns off palette shifting) (1 is default)

gl_flashblend 0 (uses normal dynamic lights instead of the orange one.
uses alpha blending i believe) (1 is default)

gl_affinemodels (0 is default)
gl_cull (1 is default)
gl_earlyswap
gl_keepjunctions (0 is default)
gl_nobind
gl_reportjunctions (0 is default)
gl_smoothmodels (1 is default)

Press the ` key again to remove command console.