There are a couple of reasons why adding an IDE controller to your system is advantageous.
1) You have 3 hard drives with a different OS on each one. You can make each one a master on its own IDE controller.
2) You have a server. You have a setup where the Primary IDE controller on your motherboard holds your boot drive as the Master, and a mirror of this drive is the slave. These drives are no more than 20GB. They only hold the OS and Programs. You have a CD rom as the Master on the secondary IDE controller on the motherboard. Then on the PCI IDE contoller you have 2 larger (60gb) drives. Your data is stored on these drives. One is a exact duplicate of the other. You have each of these drives set as masters on each of the ide controllers on the pci card.
3) For some reason you have 4 internal optical devices and 4 hardrives.
If you are concerned about your data, its always better to keep it separate from your OS and programs. You can do this with two partitions on one drive but if the drive dies, so does your data. A better way is to have a drive without any os. Its only used for data. This way, if you have to, you can move it easily to another system. Also these 120Gb drives are great on motherboards that support them. If you need to move a drive like that to an older system you may be screwed if the BIOS won't recognize the drive.