Try GTK Radiant 1.6.5
icculus.org/gtkradiant/. I sort of struggled to learn how to use it, but a lot of stuff I needed to know that wasn't in the manual I looked up here:
ws.q3df.org/level_design/. You could also try older versions of GTKRadiant
robotrenegade.com/.../downloads.html if you want, but I use 1.6.6.
With GTKRadiant you not only can make maps for Quake 3, but also games like RTCW and Jedi Academy.