uTorrent
Tiny, efficient torrenting app. Can't live without it!
I'm confused by your claim that Time Machine can't restore apps, though - of course it can! When I got my new iMac, I simply used Time Machine to restore from my external HDD that had a backup from my MacBook (with a previous version of the OS, no less). Restored files, OS setup, applications, everything - but with the new OS.
Absolutely amazing in my opinion. Sure, Time Machine is short on options - but after using it for a while I now understand why; it just works!