SATA II maximum bus throughput (per channel) is 3.0 gigabits per second, which translates to 375 megabytes per second. Only SSD drives come anywhere close to maximizing that throughput, though. Most SATA II hard drives will hover around 75-85 megabytes per second. Since PCI is limited to 133 megabytes per second with 32 bit paths, you are within tolerance unless you have an SSD. If you have an SSD, get the PCIe card.
Also keep in mind that most PCI cards will use older chipsets that might not support powerful AHCI features like native command queuing or hot swap, while most chipsets that use a PCIe interface will support these more modern features.