There are new GNU/Linux binaries for Doom3 on the ftp[1] and the BitTorrent tracker[2]. This build is compatible with the previous release, brings a number of bug fixes and new sound code. Alsa[2] and multichannel sound output are now supported.

No GUI changes were made in order to remain compatible with the first release, you will need to set some cvars on the command line to configure your sound:

set s_driver to best, alsa or oss. (best will just try alsa and fallback to OSS otherwise )
set s_numberOfSpeakers to 2 for stereo, 6 for multichannel sound ( whatever your actual number of speakers may be ).

For instance:
doom3 +set s_driver alsa +set s_numberOfSpeakers 6
will start doom3 using the Alsa sound backend in multichannel mode

notes about OSS:
The Linux kernel comes with the OSS/Free API, which works great in most cases but lacks multichannel support. You can download a binary OSS/Linux implementation from 4Front Technologies[4]. To sum up, the drivers are 'free for non commercial use'. You can use them to play Doom III. They have great multichannel support, and that's the drivers I used to develop the OSS backend.