The advantages of the raid controller is, as Riddler said, the ability to add a raid hard drive configuration. Also it alows you to have 4 additional, no-raid hard drives. So if you get a dvd and a cdrw and a cdr and zip drive you still have 4 places to put a hard drive. Disabling the raid controller in the bios, if you aren't going to use it, will speed boot-up because the raid bios isn't initialized. If you do use the raid controller as a raid controller it will take a higher percentage of your cpu's time than if you ran it as an additional IDE controller.
Clear as mud?