According to the page you linked to, the motherboard is a '9.6 inch by 9.6 inch ATX form factor'.
Wikipedia (http://en.wikipedia.org/wiki/ATX) tells me that 9.6" x 9.6" corresponds to the microATX form factor (also known as uATX.) This is a generic size of motherboard with hundreds of models available in this size.
Short answer : You're boned, because proprietary motherboards for these little media PC's are specially designed with everything placed in specific locations, so everything fits in. Buy a new motherboard with the CPU socket in a different place, and you may find your CPU heatsink needs to be in the same space as your CD drive, at the same time.
Long answer : any uATX motherboard or smaller (mATX, etc) will physically screw onto the motherboard plate, and will be electrically compatible with all the drives and other hoohah's in the computer. However, being actually able to fit everything back into the case is not guaranteed.
The question is of component placement : often with these PC's, the cases are designed to be as small as possible, which means that all the components have to be crammed in really tight. Basically, tall things on the motherboard (like CPU sockets, which have really tall heatsinks sitting on them) are placed in very specific places so that they fit *around* the CD drives, etc.
There are also the funny habits of including 'custom headers' for the hell of it, like front USB panels that terminate to ribbon cables instead of the more conventional ten-pin headers found on every single motherboard since the dawn of USB. If your computer has these nonstandard connections, you'll need some very inventive wiring to connect everything back up again.
Note - I had another look at the motherboard layout diagrams, and it looks like a fairly standard uATX motherboard layout. (My Asus motherboard in this computer isn't too different.) You can probably get away with buying any other socket 939 motherboard that has the important bits in roughly the same places (look at the overhead view and eyeball it.)
Note that if you're wanting to upgrade to a nicer CPU (i.e. a Core 2 or something), make sure the power supply in the computer can actually supply enough power to run your new processor BEFORE you buy shiny new toys.