Windows only: Veteran torrent users use helper apps to automate storage, fix file names and otherwise tweak their goods. uTorrent 2.2, in addition to improving the core product, offers easily installed "apps" that can find new stuff and fix what you've grabbed.
uTorrent 2.2's apps run the gamut from just nifty and cool, like the uMpap tool for visualising your connected peers, to useful and expansive, like the TED app for downloading those acclaimed talks, or the skinning, searching and other utilities built by uTorrents creators. Also of note in the small App Studio is a TuneUp plug-in, from the makers of the very nifty media player cleaning agent.
Along with the apps, there's now a "password-protected boss key" for instant hiding, improvements to privacy when downloading, an automated download-and-move tool for relocating finished files, and an option to pause torrents whenever user activity is detected. You can read more about what's new in this version in the forum post linked here.
uTorrent 2.2 is a free download, currently for Windows only, but likely coming soon to Mac and Linux.