Freedoom is a project to create a complete Doom II-compatible IWAD file which is Free Software.
The IWAD file is the file used by Doom which contains all the game data (graphics, sound effects, music, etc.). While the Doom source code is Free, you currently still need one of the proprietary IWAD files from id in order to play Doom. Freedoom aims to create a Free alternative. Combined with the GPL-licensed Doom source code this will result in a complete Free Doom-based game.
For more information, see http://freedoom.sf.net/