ioquake3.org is the de-facto standard in Quake 3 technology post-opensource release. Others base themselves on the hard work of the hundreds who have contributed to ioquake3. Tremulous, World of Padman, Urban Terror. All use ioquake3.org for many reasons.
Does exactly what it should. Runs much better than the version from ID on linux, plays nicely with compiz and pulse audio and didn't break anything. What else could you ask for?