I noticed that I’d gotten a couple of search requests on how to clear up the menus in Gnome. After you install a lot of applications you can get quite a lot of entries in your System » Preferences menu, and because of Gnome’s guidelines of only having two levels of menus (except for Accessibility, strangely) you get to have a cluttered Preferences menu.

The easy way is to right click on System and click Edit Menus. Then you just uncheck the entries you don’t want in the menus. You can always enable them later, if you so wish.