I was thinking about buying a bare bones shuttle machine but I was wondering whats the best way to keep it cool, without using up to much space. Are there also any general problems with these systems ?

Well the only thing you can really do is put a fan or two in, if theres room. Also are you consirned about air flow in the case/case temps or cpu temps?

The Shuttles have adequate cooling, so you shouldn't have any problems. Some older models do tend to overheat when power hungry CPU and Graphics Cards are used, but the current models are fine. There isn't any space for additional cooling so its just as well that the supplied cooling is sufficient, though you might find it noisy when the fan speeds up to cool any high end kit you've fitted.