My computer has been running smoothly for years (more than less) thanks to how I organize the hard drive. I have it partitioned so that Windows OS [Vista] is on the main partition, and the data is on the extended partition. If things get too wonky, I reimage the main partition with True Image software and go back to work.
Because of many years of moving files around here is a method that works well for me also. I organize data files into (5) five folders:
!!! TEMP !!!
Recorded TV (created by Windows Media Center)