Some motherboards have a couple different groups of SATA ports. They are controlled by different parts of your motherboard. If your board has this option, they will be different colors. As long as you keep them in the same color group, you won't see any change.
The USB ports depend on your case/motherboard. Most front panel USB ports are usb 1.1, while back panel ports are 2.0. As long as you keep them front panel or back panel, you won't see any difference.