Allmost all GNU/Linux torrents have daemons these days. I use Transmission on my server at home (it is also the default torrent client installed on the desktop), but you can also use Deluge, uTorrent and many others.
Deluge is a full-featured BitTorrent client for Linux, OS X, Unix and Windows. It uses libtorrent in its 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.
You might also be interested in flexget. It can be used with programs that use aw watch-directory (all 3 mentioned above do).
FlexGet is a multipurpose automation tool for content like torrents, nzbs, podcasts, comics, series, movies, etc. It can use different kinds of sources like RSS-feeds, html pages, csv files, search engines and there are even plugins for sites that do not provide any kind of useful feeds.