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It is proprietary. You have some options, but they are not great.
Old Shuttles frequently have problems with bad capacitors. Check out http://www.badcaps.net/ for more info. If you know how to use a soldering iron, or know somebody who does, take a look. It could be a quick and cheap fix.
You can get a replacement motherboard. Sometimes you can find a used one on eBay. Shuttle will also sell you one or do an out of warranty repair, if they have the parts. Send them an email and give it a shot. But it will be expensive. I got a Shuttle motherboard replaced twice and each time I think it was around $150 each time with shipping.
In theory, any Shuttle G-series motherboard will fit, so you could put a newer (or older) Shuttle G-series motherboard in there. But this is not really practical either. There aren't very many new G-series Shuttles anymore and unless the CPU is in exactly the same place (and I'm pretty sure they usually are not), you will need a new ICE heatsink assembly in addition to the motherboard.
A mini-ITX board will physically fit but you will have to drill your own holes, cut the back panel, then figure out how to make your components fit in the tiny thing. Shuttle designs their systems around the ICE heatsink. Put an ITX in there and the layout suddenly makes no sense. You can take a look at my thread here http://silentpcreview.com/forums/vie...p?f=23&t=60576 if you are really interested, but my basic advice is that it is not really worth the effort. There are much more interesting projects than to mod a Shuttle.