The source code release was delayed due to the whole Creative/id Software "Carmack's Reverse" legal dispute in which Creative tried to enforce a patent issue on an independently developed algorithm, which ironically still bears Carmack's name. It was the same legal dispute which delayed DooM 3's release and strong-armed id Software into packaging in Creative's EAX support despite DooM 3 already having it's own independent surround sound engine. As a result, Carmack had to rewrite key parts of the source code pertaining to "Carmack's Reverse" for the GPL release of the source code.
The Doom 3 GPL source code release does not include functionality enabling rendering of stencil shadows via the “depth fail” method, a functionality commonly known as "Carmack's Reverse".
Creative is a douchebag. Carmack is awesome. Anyway, here's the link: