Well the 32-bit install was a clean install less than a week ago and so there won't be much fragmentation. I'm using a WD Raptor 150 (it's about 1.5 years old, but still runs great and at 10k RPM).
What do you mean by "dirty upgrade"? I'm considering wiping it all out and starting from scratch with the 64-bit OS, but that will be another 2 hours I'd rather spend playing SC2.
The system runs slower all the time, even for file access and Windows explorer.