PCI SATA Controller Speeds
 

Would the speeds of hard disks connected through a PCI SATA controller be limited by the maximum speed of the PCI bus?

In general, even onboard controllers still use the PCI bus. But either way, the hard drive is generally the limiting factor, unless you make some absurd RAID array. And in that case, you can probably afford a new mobo with SATA and PCIe. =P

Of course it's limited. You should also think about other devices on the PCI bus. There's the soundcard which also uses a lot of bandwidth, then probably a network interface and so on. And most of the time there isn't just one drive connected to the SATA.
Put in some overhead and you maybe end up with the PCI as bottleneck.