Well, if you want the ability to upgrade aka, swap motherboads out and such, you might want to look at doing an Aria/m-ATX setup as it gives you the ability to change motherboards like some of us change underwear.
The Aria case will hold three hard disks as well as an optical drive. The m-ATX motherboards will give you the ability to add three PCI and one AGP setup so it has a bit more expansion options then that of Shuttle/Barebones XPC's.
The nice thing about the Shuttles though is that its an all in one solution. You don't have to go hunting for a motherboard that supports USB2.0/Firewire, and you know all the connectors on the front of the case will work since the supplied motherboard was designed to work in that particular Case.
You said under $1000, but what platform (AMD/Intel) were you looking to buy?