Application: Bittorrent Sync
Developer: Bittorrent, Inc.
License: Freeware, not open source
Description: A syncing program built on the Bittorrent protocol.
Leaves settings in %APPDATA%\Bittorrent Sync. As far as I can tell, there is nothing stored in the registry.
Since it shares a majority of its code base with uTorrent, I think that it would be reasonable to make portable. I don't have the time to repurpose the uTorrent Portable code myself, so I'm seeing if anyone else can do it (if they find value in it). The one major hurdle I can foresee is how Bittorrent Sync handles the sync keys. I don't know how bound they are to a particular folder or drive.