They have to do with the interface between your computer and the harddrives.
Read this: http://en.wikipedia.org/wiki/Sata
That being said, the actual hard drive also plays a big factor in determining the performance of your system.
For my next system, which I will build soon, I will actually buy an IDE harddrive. When I have more money, I am planning on getting 2 74GB Raptors in Raid 0 (sata), and using my original IDE drive as an external backup. The performance for a 7200 rpm shouldn't be that different for SATA and IDE IMO.