Trenchbroom is a GPLv3 full 3D map editor for Quake and available on Windows and OS/X (Sources only for Linux) by Sleepwalkr:

Features:

- True 3D editing, no 2D views required
- High performance renderer with support for huge maps
- Vertex editing with edge and face splitting
- Manipulation of multiple vertices at once (great for trisoup editing)
- Smart clip tool
- Move, rotate and flip brushes and entities
- Precise texture lock for all operations
- Smart entity property editors
- Graphical entity browser with drag and drop support
- Comprehensive texture application and manipulation tools
- Search and filter functions
- Unlimited undo and redo
- Point file support
- Automatic backup
- Support for .def and .fdg files, mods and multiple wad files
- Free (as in beer) and open source (GPLv3)
- Cross platform (Windows, Mac OS X and Linux supported)

Links: Official site, Download trenchbroom, Official Trenchbroom video, Announce on Func, Trenchbroom videos by deqer