iD has released the much anticipated, Doom 3 SDK. The more technically minded fans of the game will now have the opportunity to work on their own custom mods for the game.
SDK site is here. Here are a few tips from the biggest Doom 3 modders of them all, iD Software.
If you plan on modifying Doom 3 at all, I highly recommend installing it in C:\Doom3. A lot of the built in tools get really upset if there are spaces in the file name, so installing it in "Program Files" is not really an option.
As for the pack files, I recommend leaving them packed up, and only unpacking the files you need. This will keep your install pure so you can play on pure servers, and it also keeps your directories clean. It makes the things you modified much easier to find than if there were a bunch of standard id files laying around. Since the tools (like DOOMEdit) are all built in to the game, they don't care if the files come from the directory or from in a pack file.
I would also recommend keeping all your modified assets in a seperate folder, such as "mymod" rather than in "base". This makes reinstalling much easier and allows you to seperate your stuff that you're working on from the default game stuff and stuff other people have made. You can create a shortcut to Doom 3 with +set fs_game mymod in the "target" so you don't have to keep selecting your mod every time you start the game.