You will have fewer SATA and USB ports. The BIOS might be more clunky. You won't be able to install as many pci-e cards. You won't be able to overclock at all or as well. The CPU will run basically the same-the difference is in what ports and connectors will be available. The onboard chips controlling audio, drives, and networking are usually not as high quality.
For most users, it wouldn't make any difference.