A few I can think of Trenchbroom (Quake/Quake 2/Hexen 2/Daikatana), Mapster32 a part of EDuke32 package (Duke Nukem 3D/Blood/Shadow Warrior/etc.), GTKRadiant (Quake/Quake 2/Quake III Arena/QuakeLive/Return to Castle Wolfenstein/Star Trek Voyager: Elite Force/Star Wars Jedi Knight: Jedi Academy/Wolfenstein: Enemy Territory), Hammer for Source Engine games.
I'm sure there plenty other I don't know about