Boot up to the reinstallation CD. You will have to hit any key to get it to finish booting up to the CD. You eventually will get two or three questions. Hit Enter to re-install the Windows XP. Do not hit "R" for repair on this screen. You will then hit F8 key when asked for it. Later you will get a screen with more options. on this one, hit "R" for repair. Do not hit "esc" which will lead out to formatting your hard drive. This will wipe out the Windows OS and re-install it, but will not wipe out the other software.
After completing reinstallation, you will have to "update" your Windows. If you have a SP3 CD downloaded, you should install this first. After that, simply do the "update" over and over until there are no more updates needed.
Note: If you are doing this, make sure you don't do anything that causes your hard drive to be formatted. You will get notice of formatting steps so you will have to approve the step for it to format.