I use a bat file.

@echo off
echo Quake + expansions
echo 1: Quake
echo 2: Mission Pack 1: Scourge of Armagon
echo 3: Mission Pack 2: Dissolution of Eternity
set /p userinp=choose a number (1-3):
goto %userinp%
:1
goto end
:2
set game%=hipnotic
goto end
:3
set game%=rogue
goto end
:end
Winquake.exe -game %game%

If you need a cd I still have the .nrg files and the install files.