Saw this list online, I'm sure there's more.  Most of these are based on modified versions of the Open Source Quake projects.  I haven't checked these out yet, but will be soon!http://alientrap.org/nexuiz/
http://www.urbanterror.net/news.php
http://cubeengine.com/
http://openarena.ws/
http://tremulous.net/
http://www.warsow.net/?page=home