id Software has released Quake3 v1.32 which includes PunkBuster support to stop all the cheaters. Read what's new! Here are the download links:

Quake3 1.32 Windows
Quake3 1.32 Linux

When first installed, PunkBuster will be disabled. To enable PunkBuster so that you can join PunkBuster enabled servers, click 'Multiplayer' from the main menu. Find the clickable item in the upper right portion of the in-game server browser screen that says PunkBuster: Disabled and click it.

Commands:

cl_punkbuster 1 <-- for clients
sv_punkbuster 1 <-- for servers