In the System folders section you have the following options:
Windows have certain folders for certain purposes. My Documents for instance is called Personal by Windows. I have changed it from My Documents to Temp. Works perfectly and one less folder in the root. This option helps you do this, you can move the Favorites folder to another drive, so if you format the Windows drive you will still have your favorites. You can move many directories with this option, but there might be some folders that works best left alone, of course you can always try and see what happens, it is possible to change it back.
Do it like this, select the folder you want to relocate, you will see the path below the list. Double-click on the selected item and a dialog opens. On that dialog you can either write the path to the new folder, or you can do it the safer way, by clicking on the browse button and browse to the correct folder. It's quite easy to misspell the path if you want to enter it manually.
In the Autorun programs section you can do the following:
You can delete the autorun programs in the registry and in the Start Menu. If you aren't certain what a program does, just leave it alone. There is also the possibility to disable programs. That means that you can enable the program again if you see that the program's auto start is necessary. Do this by removing the check mark in front of the line. If you can't figure out what program an entry starts, you can always select it and click on the Edit button, then you can see what file the entry starts. If you feel like it you can also change the entry. NOTE: It is not possible to edit the entry of a Start Menu program.