Are you sure you effectively shut down all the tasks? I know that right at start-up there are already half a dozen tasks running, mostly just preloaded google apps. Just install a task manager to see this for yourself.
When you don't see anything running, there are actually a dozen different things running.
I've tested my theory on 2 different gentouches. After advanced task kill killing off all those silent but deadly running tasks, the device was considerably cooler than before. Yes, it's still warm, but not hot. And battery life was way up.
anyways, just to clue you in:
rooted, market hack, clockwork, update.zip, setcpu plus a bunch of other modifications using inbuilt system settings ATM...
I guess your gentouch is different than mine, then. I was using it outside today in 82 degree sunny sky today and it never felt unbearably hot. Yeah, it heats up like every other tablet-like device that size. The ipad's been having heating issue, too, you know.
Added by edit.
I wonder... is there anything wrong with adding a few holes of our own? It's just plastic casing.