I linked to that processor because it seems to be the sweet spot right now. You can go faster on AMD but you'll spend three times as much.

Frankly, there aren't a lot of choices in Shuttles. Not if you check off some big items in your mind. First choose a processor. If you're going AMD, go with either the SN95G5 or the previously mentioned SN25P. The first is smaller but the second gives you more expansion options (except it doesn't have a PCI slot). The SN25P also has 6 USB ports, which you said was important to you.