I've noticed that Time Capsules can really run hot. I haven't figured it out, but it looks like something keeps accessing them. "Speculation":http://discussions.apple.com/thread.jspa?threadID=1428330 is that if you have the Time Capsule drives mounted on a Mac, then the hard disk stays spinning.
I've had mine stacked and that seems to be bad too. You want them to be separate and some folks put them on little legs to get ventilation underneath. I unstacked them and they are much cooler now.
"Macrumors":http://forums.macrumors.com/showthread.php?t=481793 found that they are 114F or 45C when they are just sitting there standalone and when stacked they are warmer still. The main issue is that the Time Capsule fan blows downward and it isn't effective and small, so it needs to be a little higher to work. A couple of pairs of nickles seem to help to give it a little height.