Look here. I used it once to migrate internet explorer stuff and outlook stuff to a new system.
Also you could use TweakUI to look at the maps where the most important personal files are stored on your system.
I recommend keeping the old partition in place or make an image of it by ie. using Ghost. If there's anything you missed after the reinstall, you can still easily retrieve it. For a Win9x platform you should beforehand boot into DOS and rename the progra~1 and windows to *.old Then you can start with the reinstall.
Hope this helps in some way, I know it's a pain to do this, good luck!

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Edwin de Vaan