My current SATA HD (WD2500JD) has SSC enabled. It was installed that way in my Gateway. It has an Intel D926GAG motherboard.
My new HD is a SATA2 WD5000AAKS.
I'm looking to do a fresh install on the new drive to boot from a new SATA2 Card (which has a RAID option, for future use).
"Sounds" to me like you can just take off the jumper and turn it off. It cuts out EMI sound interference - keeps the drive from possibly sending spikes of electrical noise to other drives or devices. Can't see it doing anything worthwhile in home/office system - perhaps if you were running in a nuclear lab!
Seagate seems to have a SSC software option that's very complicated, but I believe WD just has the jumper and it won't affect anything.