I am building a server that will benefit from SATA III, but the motherboard that I will be using only has SATA II support. As such, I was considering using a SATA III card on my motherboard. My only concern is the interface between the motherboard and the card. I have four hard drives to connect, with more to be added later as needed. Most of the cards that I have found are PCI-E x4 or x8. Will this "bottleneck" the data transfer?
SATA-III (6Gbit/sec) is overkill for hard drives, since their platters don't rotate fast enough to even get close to SATA-II (3Gbit/sec) speeds. They'll work just fine, but I wouldn't spend any extra money on SATA-III for them. If they're high-end SSDs then SATA-III may be required for full performance, but for hard drives SATA-II gives you way more throughput than you need.
A 4X PCIe can transfer data at around 1GBit/sec, so it could theoretically handle four devices simultaneously transferring at around 250MByte/sec.
If all of your SSDs have transfer rates north of 250MByte/sec, then connecting four of them to a PCIe x4 card could be a bottleneck. But I don't think it would be all that serious - you'd only experience the bottleneck if all 4 drives were transferring large blocks simultaneously - that probably wouldn't happen all that often unless you have some unusual I/O requirement.
If it's an issue, a PCIe x8 card ought to eliminate any worries.