Running them seperate can be nice for performance too. I used to run a large file server back in college (on an I2 connection no less ^^). Before I banished the file server dirs from my paging and program files disks I was getting really terrible performance and noticeable lag. This especially applies to IDE/SATA drives since they suck at multiple requests.
So if you run a server, keep P2P stuff open in the background, or work with lots of or large size files moving around a lot, etc and have noticed your system just isn't quick and snappy anymore then splitting your usage across multiple disks can bring it back.