You are all focusing merely on the heat, rather than the actual problem: his CPU unusually going full-whack. Obviously a CPU at full-whack will get hot causing the fan to kick-in, therefore it's kinda obvious that things would slow down, since the CPU is at full-whack.
Not sure what the problem is, but I certainly wouldn't poke around with the hardware; there was no harm in looking, which you've done, so that's good. I would look at software, and I would double check the BIOS is all set right.
BTW, your CPU, the Phenom II, commonly has heat issues; my previous 965 Phenom II was a nightmare with heat, and so I ditched it for something much better. I don't think it's heat at all, though.. just felt like adding what is probably pointless info'.
Try running the OS in safe mode for a while, and make sure to see whether it does the slow down; if it does, worry a bit, then temporarily try a restore point from a time before this problem occurred, and if it doesn't, well.. still try the SR. Since I don't know your OS settings, your software, and any hardware settings, I couldn't recommend much else, other than a system restore. (you should be able to undo the SR, if you get no luck with it.)
OP, it might actually be worth posting your CPU temps, just to absolutely rule that out. (sorry if you already have.. didn't read all the posts, since I have a headache and can't be bothered to do heaps of reading)