I found a great article today at TorrentFreak on enabling encryption for several popular BitTorrent clients. My personal client is Azureus, however BitComet and uTorrent are included as well.
The first thing you may have to do before enabling encryption is to change your User Proficiency to something above the rather noobish Beginner to at least Intermediate. Once that is saved you will have access to the encryption options located under the Connection menu.
With bandwidth shaping in full use by many greedy access providers enabling encryption may increase the speed of your BitTorrent downloads considerably. I can’t say from personal use that it’s increased my speeds which are provided by Comcast Business, but I’ll keep an eye on it and report any significant jumps.