The idea is to have your operating system installed on the fast drive (the SSD or the Raptor). Any program files, games, applications you install will be stored here and run from here. You take advantage of a really fast read/write, while not wasting money on space that you won't be using.
Then, you get another drive strictly for storage media. This way you can get a cheap 1TB+ drive. Personally I like the WD Caviar Greens cause they run quiet, cool, and power efficient. This won't effect performance of your computer.
The way I have it set up is I have a 10,000RPM WD raptor for my OS, and I have 2 x 1TB WD Caviar Blacks set up in a RAID 0 to make a 2TB drive, and I back that up with a 2TB external.