it depends on the Sata controller (and this is the reason why there is a speed jumper). Especially Via Sata controllers couldn’t handle the newer Sata II HDDs. To get such a HDD running, the drive must be set to the lower speed.
That said, make sure that the Sata controller is capable to deal with SataII HDDs. If not, then leave the jumper as is.
Additional note: I don’t see any noticeable advantage if the HDD operation mode is changed to “3GBps” via jumper.