As I think you already know, it's annoying to see that Firefox ignores you when you tell him that you want ALWAYS to use THIS program from now on. (i'm speaking about the checkbox of Firefox's download manager, do this automatically for files like this from now on). I've edited the preferences, the mime types, but without any luck..
There are a lot of good BitTorrent applications for Linux, but some people just don't want to give up uTorrent because either they are too used to it or just because it actually works quite OK in Linux, under Wine. One major problem with using uTorrent this way is that Firefox doesn't open .torrent files with uTorrent, so you have to save the torrent file and then load it.
Ubuntu Tweak is a utility created to make it easier for users to configure and change a variety of system settings. You can use it to quickly adjust settings for GNOME Panel, Compiz, and Nautilus, along with some more advanced security settings.
Do is an application to find things on your system and quickly perform actions, similar to Quicksilver for OSX and GNOME Launch Box. It works on a variety of different desktop environments, including GNOME and KDE. Basically, all you need to do is to press Super + Space on your keyboard, and the Do dialog will open. Super is the Windows key on a PC, or the Command key on a Mac. Type in the name of an application, and Do will launch it for you.