Haven't officially started this project yet, but I have nailed down a .MAP renderer (which was the hardest part). Currently it's incorporated into my game engine but it will be ripped out to make this standalone tool, which will be available on Subversion when I get a webspace.
This tool will be a rudimentary 'level of levels' editor. You import entire levels as .MAP files and can move them around, or rotate them at 90 degree increments (yaw only). So if, say, you wanted to put all of Quake singleplayer into one big map, you could use this tool. Import all the maps, create some connecting pieces in a map editor and import them too, remove a few brushes (like the backs of the dark doorways), fiddle with some entities (mainly changelevels), and export! Then try to find a compile tool that can handle such a massive level.
Some things will be handled natively, such as renaming target/targetname pairs to mapname_targetname, and changing slipgate changelevels into teleports. It remains to be seen how well having thousands of monsters waiting around the map will work. It will also be interesting to see how this works out in multiplayer...
For screenshots of the .MAP renderer, see:
(the white textures are non-power-of-two ones that I forgot to scale up)
Of course when editing only a few maps at a time will need to be rendered.
The interface will all be SDL and OpenGL, no OS-specific GUI stuff. I don't know yet if there will be 2D viewports, but the 3D mode will have a few different control schemes - FPS noclip controls, Maya controls, WorldCraft controls, UnrealEd controls are planned. There will be a 3D snap to grid feature.