I've got a similar spec to you, but don't have any real problems. My machine is as follows.
GA-MA790FXT-UD5P board with Phenom II X4 955BE
8GB (4 x 2GB) Corsair DDR1600 RAM manually set to 1600 with timings and voltages detailed by Corsair.
Gigabyte made ATi HD4670 graphics card
2 x IDE hard drive
3 x SATA hard drive
1 x solid state SATA hard drive
2 x DVDROM (1 is BluRay capable)
1 x Adaptec 29320A U320SCSI controller with SCSI ZIP drive
I very occasionally get a freeze during POST (normally when checlking the memory or drives) or during initial Windows boot, but a reset always fixes the problem. I suspect this is BIOS related as I'm still on F5 and I think its a clash between the SATA and SCSI drive controllers as I had to remove the SCSI hard drives and CDROMs I originally installed as they would go into a continual bus reset loop slowing the machine to a crawl, but that's another story. As my configuration is now it almost always boots first time and freezes and crashes are very rare. I'm running Windows7 RC1 64bit (will be upgrading to the official release in the next couple of months) along with Windows XP 32bit and SuSE Linux 11.1 4bit. I've also got a tiny partition with MS-DOS6.22 housing the boot manager!
Not only is the system stable with the processor at a stock 3.2GHz, if I change the multiplier I can get up to 4GHz and remain stable, although I'll admit I've only done this a few times for no more than an hour under normal loading. Possibly stress tested it would fail or get a bit too hot, but at stock speeds its quick enough so I'm saving overclocking for later on when it begins to feel sluggish.
I'm also running the stock AMD cooler as most replacement coolers are too big and overhang the memory slots, which is no good to me as I'm using all of them. The CPU generally sits around 30-35DegC, pushing up into the low 40's when worked hard. I may change the cooler later on if I can find a comact one, but I'll be specifically looking for one that blows air over the mainboard heat sinks. After all, there's little point having a cool CPU if the chipset begins overheating!
I've not had the fan not running problem, but I'm on BIOS F5 which does appear to use the minimum fan speed from EastTune6 (I'm set at 31%). I will probably upgrade the BIOS in the future, but as things are stable at the moment I don't see the point of messing it around. Just one thought. Have you tried installing EastTune6 (latest version) and manually set the fan controls to see if this has any effect on the fan? I'm just wondering if the settings in EastTune6 get written into the CMOS to be used when the machine is next booted. Certainly if you enable cool'n'quiet it uses the reduced voltages and processor speed controls on the next reboot even if you don't have cool'n'quiet installed or boot into a different operating system where cool'n'quiet is switched off! Again, this might be to do with the F5 BIOS, so manually setting the fan control using EasyTune6 may not work for you.