rTorrent / ruTorrent

rTorrent (with the ruTorrent web interface) seems to be the best choice so far. Great interface, lots of options. Both the main program (rTorrent) and the web interface (ruTorrent) are available in Portage. ruTorrent can be installed via webapp-config.
The best is to create a separate torrent user. The main configuration file for rTorrent is ~/.rtorrent.rc. An important directory must be created for the rTorrent session - it contains all torrent files and the relevant configuration information for each torrent.
There is no init script available, so best way to load rTorrent is to run in a screen the following command:

sudo -u torrent rtorrent

then detach the screen.

To quit rTorrent via the command line interface, hit Control + q (several times may be needed to force a shutdown instead of a graceful shutdown). However, this does not always work, if rTorrent gets stuck, you need to kill the process.

DHT

DHT allows trackerless torrenting, ie peers connect directly to each other without the supervision of a tracker. Most private trackers disable DHT in their torrents, but it can be useful for random torrents found on the Internet when the tracker is long gone but peers are still seeding the file.

On ruTorrent, DHT is disabled by default but can be activated using the web interface easily.

Vuze has a buggy and outdated web interface, mostly because it is written in Java (applet). On recent versions, it does not work at all. Not a good choice for a server.