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No, it is a stand-alone application, unless you use the installer version. However, on first run, it will ask if you would like to make shortcuts on your start menu and desktop.
They are stored in %AppData%\uTorrent. The .torrent files you load are stored there so µTorrent can keep track of your torrents.
Delete the exe. If you're concerned about the settings being left on your PC, delete the folder uTorrent in %AppData%.
Simply copy settings.dat (located in %AppData%\uTorrent ) to the same folder as uTorrent.exe, and you're done.
Simply copy the entire contents of %AppData%\uTorrent into the same folder as utorrent.exe. Alternatively, create a blank file named settings.dat in the same folder as utorrent.exe, if you'd like to start out fresh (no settings/torrents). If using it in a multi-user environment, this folder should be accessible and writeable by all users so they can share settings and resume data.
Simply make a copy of the entire %AppData%\uTorrent folder.
Delete settings.dat and settings.dat.old from %AppData%\uTorrent with the client closed.
Put tray.ico (for the tray) and main.ico (for the GUI) in %AppData%\uTorrent, or in the same directory as utorrent.exe if you have the settings in the same directory. You must restart µTorrent for this to take effect. There are a selection of icons on the Skins page and User Interface Design section of the µTorrent forums.
Visit the Skins page and the User Interface Design section of the µTorrent forums for skins and instructions on creating your own. To use them, place them in %AppData%\uTorrent and restart µTorrent.