I know I'm resurecting an old post here, but you guys have helped me so much with my feeble coding; I thought you may benefit from what I do.
I understand what you mean that a totally clean Windows is the best - but takes hours to load and set up the way you like. [All those endless Shutdown and Restarts after every piece of software...]
Firstly, I partition my hard drive with three partitions of 25%, 50% and 25% and name them C: - XP System, D: - Data & E: - Ghost. I then build my clean windows on C: and when finished - do a 'Partition to Image' with Norton Ghost and store the image on the E: drive.
Now if something hits my system; I use 'Image to Partition' and I'm back up to that clean Windows in under 10 minutes. Keep your Ghost Image up to date and clean by doing an Image to partition before loading anything new and re-image straight away if the new software works OK. Another fantastic feature of Ghost is when its writing your image, all sectors are physically written in the correct order - so no matter how badly fragmented your Windows partition was when you imaged; its like it performs a fulldefrag when writing back your image.
Also, all of your data; stored on the D: Data drive, stays intact throughout the above process and lends itself to easy backup to external drives or DVD because its, well, just data.
Christopher