My choice BitTorrent client for headless Linux NAS server - Transmission has recently got a nice feature upgrade. Transmission already had most features you want from a BitTorrent client: encryption, a web interface, peer exchange, DHT, UPnP and NAT-PMP port forwarding, web seed support, watch directories, tracker editing, global and per-torrent speed limits, and more. Now it finally supports magnet links, and for users switching from Mac desktop client - the dearly missed "turtle mode" in Web UI!
I have described Transmission installation procedure on Ubuntu Jaunty (9.04) using PPA repository. If you went this route instead of installing package from default Ubuntu repository, you're all set for upgrade. Simply run:
$ sudo apt-get update $ sudo apt-get upgrade