Quake 3 Links
Dragonball Quake
Dragonball Quake is the mod I most want for Quake 3. I put the link here cause I think its too good to miss. It hasn't been released yet.

QeRadiant
This is the site to go to to get Q3/GTK radiant. Also has all the latest updates as well as lots of mapping tools, textures etc.

Half Life Links
Quark
Quark is another powerful and popular mapping tool for Half Life and Quake engine based games.