If you are a member of a lot of different private trackers organizing your torrents with groups is an absolute must. I like to have 3 groups for each tracker, one for current downloads, one for torrents I’ve uploaded myself, and a third for torrents I’m seeding.

I also find it handy to have Transmission watch my Desktop (or whatever folder you use for downloads) for new torrent files. I tell Firefox to automatically download them there, Transmission opens them, and I put them in their group (make sure to have the ‘add window’ display. Its helpful for keeping torrents organized). Then I have Transmission set to automatically move added torrent files to the trash.