You don’t need a cracked EXE anymore. Here are the legitimate ways to play Quake 3 Arena without a CD today:
Updating your game to the latest official version is the standard method to enable play without a CD. Download the Point Release 1.32 Quake 3 Arena No Cd Patch
Quake 3 Arena is available DRM-free or with minimal launchers on: You don’t need a cracked EXE anymore