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Out of the box you will find a Doom3 entry in the indieGO games menu.
Before you will start you need the game data files from an original doom3 dvd or buy it from here http://store.steampowered.com/app/9050/ or http://store.steampowered.com/app/9070/ ( Resurrection of Evil )
CD 1 /Setup/Data/base/pak002.pk4
CD 2 /Setup/Data/base/pak000.pk4
CD 3 /Setup/Data/base/pak003.pk4
I've bought it from Steam because it has also applied the latest patches to it.
if you have all these files from original CD or DVD or any other source mentioned, it has to go into ~/.doom3/base folder
Doom 3 Resurrection of Evil files has to go into ~/.doom3/d3xp folder
after this you need the latest updates for doom3, you can get it here:
extract files and copy them over to doom3 base folder
sudo chmod 755 doom3-linux-188.8.131.524.x86.run
./doom3-linux-184.108.40.2064.x86.run --target .
mv *.pk4 ~/.doom3/base