All your personal files/documents will remain, but 98se will revert back to it's original settings that are on the CD, you will need to update your drivers and windows files again.
If you want a nice clean start, then better to backup, or have access to all your drivers and files, also make sure you have access to all your programs that you have installed over the past few years.
Format your drive and start again with a clean install. This will remove all the rubbish that has been collected and your system will fly along like new. j.