I see some talk of this from searching the wiki. In the OSX version you can assign color-coded groups to transfers, making them easy to filter out and visualize. This feature is fantastic for dealing with transfers with various private trackers. I make extensive use of this feature as I have many active transfers.
- Colored progress bars
Green for seeding, blue for downloading, gray for paused, orange for verifying. Gives a very apparent and intuitive indication of a transfer's status. Very helpful.
- The "Keep Incomplete files in ____" option
Allows you to specify a location to keep incomplete transfers. Keeping incomplete files separate is important, as you might accidentally work with them otherwise. At a glance I can look at my file manager and see what is finished and ready to be watched/listened to/installed/shared. Strange that this one is in the OSX version but not the GTK+.
The first two of these features I think are more important than some realize. I've introduced many people to BitTorrent, and of those people, the ones who start with Transmission on a Mac seem to fair much better. Those who use other clients get lost and discouraged, running home crying to a more familiar p2p method. To me, the reason for this is obvious. Whereas 'Power Users' can make do with some text on a CLI, more casual computer users need a friendly and intuitive interface. We all know this is one of those things keeping Linux and BitTorrent from complete mainstream dominance. I don't mean to suggest that Transmission devs should be burdened with such things, however. I just happen to think these kinds of features are very important while the world of open source tends to favor bare functionality over having a nice GUI. Transmission is so good (oh yes it is) because it's a fully capable client with a simply-but-deadly interface, so let's not forget that!