Linux BitTorrent client with support for magnet links
rTorrent has support for magnet links since v0.8.7 released in October 2010. To load one, just hit backspace in rTorrent and paste the magnet information.
The information provided below is three years old and outdated.
Maybe the tutorial How To Compile rTorrent From SVN In Ubuntu 9.10 Karmic Koala / Debian 5 Lenny With Magnet Link Support will help you.
Also, Transmission development version 1.80b1 supports magnet links. See changes.
Deluge 1.1.9 supports magnet.
Deluge is a full-featured BitTorrent client for Linux, OS X, Unix and Windows. It uses libtorrent in it's backend and features multiple user-interfaces including: GTK+, web and console. It has been designed using the client server model with a daemon process that handles all the bittorrent activity. The Deluge daemon is able to run on headless machines with the user-interfaces being able to connect remotely from any platform.