I don't have any evidence to back it up, but I think uTorrent has better network code and produces faster downloads. I use despite its slight ugliness compared to transmission.
After trying many clients, I have settled for rTorrent (libtorrent.rakshasa.no) which is quite lean and terminal based (so that I can wrap it in a Screen session)
The uTorrent people say they're working on a Linux version, but haven't given details. Until then, it works well under Wine. Or there are a lot of other options, too.