Your problem isn't really all that uncommon - I've encountered lots of machines that became cantankerous after running for a lengthly period. Often you just have to use the power switch in the rear of the case (or pull the power cord if it's an inexpensive unit w/out the switch) to power it down completely, then do a cold-boot after a while. Even with WinXP + SP2 and all the updates, I like to cold-boot my machine twice a week, just to keep it fresh.

Other (more extreme) cases need a Windows refresh (reinstall) to clean up some random garbage that's infested the machine, so your milage may vary. But I wouldn't worry too much about damaging your hardware - that's very unlikely.