A friend also had heat problems, the CPU even switched itself off
Now these things can do this, as I was using an Athlon XP suddently the taskbar in Win XP went black, then after I closed some windows there was more black. I pushed the reset button and took a look in the BIOS - 92°C !!! The fan stopped without reason. But this processor is still working!
There are various AMD stock coolers, the aluminium based ones had only two series which are really quiet. I know the bigger coolers for the Athlon FX and Opteron series, there are two versions, one has all heatpipes on one side and the other one has two on each side. They also differ in rotation speed. Which version do you have? Do you have the older version with the holograph on the fan?
There are a lot of reasons if a cpu has a high temperature. If you want to test another fan I can recommend the Scythe Shuriken. It is very small (64 mm height) and absolutely easy to mount. And use some good thermal grease, I'm using Arctic Silver 5. I only apply one pea-sized drop in the center of the cpu and some small drops in a circle around it. While mounting the cooler I twist it a bit on the cpu, so the grease will become only a very thin layer. But beware: This stuff is sticky as hell. It needs some cleaning sessions for cpu and fan, even when using isopropyle alcohole. If you hate someone, press him a tube Artic Silver 5 in the inner pocket of his jacket. He NEVER gets out everything
Another thing is the airflow in the case. I'm only using a 8 cm fan at the backside and a Sharkoon Silentstorm power supply which has a 9 cm fan on the bottom and an 8 cm fan at the back. My gfx cards are all passive, so they should produce more heat, but it doesn't seem to be problematic. My harddisks (I've got 3-4 in every computer) are all from Samsung, they have a temperature around 37°C. You can touch and carry them after hours of using, try this with an Hitachi HD which gets up to 55°C! I'll now add another 9,2 cm fan before my HDs which keeps the heat from getting in the inside.
Here's a list of my favourite manufacturers and products, all components are very silent.
CPU coolers: Scythe Shuriken, about 25 Eur (Mugen is too big for standard cases)
Thermal Grease: Artic Silver 5, about 5 Eur
Case fans: Sharkoon, about 6-8 Eur
Harddisks: Samsung, highly recommendable is the Spinpoint HD103UJ, it's amazing fast, quiet and cool. I got them new for 73 Euro!!
Power Supply: Sharkoon Silentstorm 480W Dual-Fan, on ebay about 25 Eur. 480W seems to be a bit weak, but this thing has a combined power of 384W ! You can buy a 700W PSU, but if it has a combined power of only 115W then it's crap, if you have a big cpu and gfx card it may even not be able to start the computer. The other power supplies I'm using for my other computers are no-names from x-super, 550W and combined power of 235W. The Sharkoon Silentstorm is also interesting because it has very long cables for the CPU power supply, good for Bigtowers and for fullsize-ATX-HTPC-cases which have the PSU at the front (like mine).