Unfortunately, the simplest,safest and most reliable fix for most "windows related problems" is the clean install (with drive formatting). If you opt to do this, I would also recommend that you install a removeable drive bay and specialize your drives into 2 categories ...
1. Primary OS drive (with apps)
2. Data drive
This has a number of potential advantages for system reliability and performance.
1. Since your drives are separate, you can tailor the size and speed of the drive for the best blend of performance to cost ratio ...
Use a WD raptor for your for performance (10,000 rpm sata 72/150 gig) can be had for relatively cheap (considering performance factor) ... if you can find the 36 gig raptor for cheap better yet.
Use a good 7200 rpm high cap drive for economical data storage.
With a multiple drive setup and at least 1 removeable drive bay (os drive) allows for a very convenient backup strategy of utilizing a 3rd drive (that is cloned) to be used in case of dire emergency.
Say if your OS goes bad (virus/bad sector/registry muckup etc) ... simply remove the OS "cartridge" (hdd mounted in removeable tray ... and insert in the fresh cloned OS with apps ... for all in intents and purposes, your system will then undergo a clean "brain" transplant in minutes.
Alternate (read) cheap method ... simply mount the cloned drive next to the OS drive in the case ... if you start to develop serious or unrecoverable system probs with your original drive, simply shut down the system, open the case and plug in the cloned drive (sata/power cable)... restart your pc and viola ... it lives.
Note that if the originating problem is some kind of virus or trojan that has found its way into your data drive, then exercise basic caution in how you activate your virus protection cycle. The safest that I have found is to use a disk based OS/virus scanning strategy as an initial scanning requirement.
Of course, this begs the basic question ... why not just create an emergency partition on your drive with the backup on it ...would this not save the time and expense of a additional hdd? Well, the short answer would be yes ... but at the question of drive reliability and the possible need for the usual proprietary "bootup" device in the form of floppy/cd/dvd/flashdrive which is used to jumpstart the OS switchover from the failing partition to the :new" one.
Personally, I have greater peace of mind and reliability with a totally separate (read isolated) fully loaded and uncompressed OS just waiting on the proverbial bench.
I think therefore I am ... I think :/