Putting your OS on one drive and your programs on another physical drive (as opposed to a different partition) will give you better performance. Your computer will be able to access both drives at the same time with full bandwidth instead of acccessing one and then the other.
As said above, putting data (music and other files) on a separate drive keeps it safer than not. If your system disk dies, your other data is still there on the other drive.
Of course there are other options such as the different flavors of RAID that require multiple disks and various benefits, as well.
Plus, you can never have too much storage space.