Enter this into the terminal:
$ gconftool-2 -t string -s /desktop/gnome/url-handlers/magnet/command "ktorrent %i -caption "%c" %u"Change what is comas with your preferred torrent client.
$ gconftool-2 -s /desktop/gnome/url-handlers/magnet/needs_terminal false -t bool
$ gconftool-2 -t bool -s /desktop/gnome/url-handlers/magnet/enabled true
If you entered the above correcly you will end up with a new entry in gconf-editor like so:
Remember that mangnet links take a little longer to start downloading, just be patient.