I prefer Deluge. Stable enough for me.

uTorrent. even on Linux.

Actually you can customize bandwidth for individual torrents on the recent kde4-based versions. Simply select "speed limits" from the downloads menu (hotkey Crtl+L) and you'll get a dialog which will let you set the download and upload limits for each torrent separately.

There appeared to be a bad memory leak recently in ktorrent, because after a few hours it would occupy almost all of my ram+swap and slow everything down to a crawl. But I updated to the most recent v3.14 from the Debian repositories and now it's been running for several straight days without stressing my (fairly old) system at all.

I use rtorrent mostly, but there's the occasion when I use deluge too.