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.)
G'luck.
EDIT:
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)