Which torrent apps work headless (from command line only)?

You should take a look at this wikipedia entry. I've used rtorrent and i liked it.

You should look at deluge. It is cross-platform, and is excellent as a headless app.

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.

Deluge features a rich plugin collection; in fact, most of Deluge's functionality is available in the form of plugins.

Deluge was created with the intention of being lightweight and unobtrusive. It is our belief that downloading shouldn't be the primary task on your computer and therefore shouldn't monopolize system resources.

Deluge is not designed for any one desktop environment and will work just fine in GNOME, KDE, XFCE and others. We do our best to adhere to the freedesktop standards.

I have the deluged daemon run as a service on boot, and also run a client on the same machine that hosts the web interface. I then use the web interface from all my systems.

For Unix-based systems you can use rTorrent.