If you know exactly what files are missing you can replace them from the install CD, or copy them from another system of the same family (ie. don't replace WinXP files with Win98 files)... or mount your primary drive as a secondary drive and copy them over that way. It is possible...
However, if you're not sure what files are missing and you're having lots of strange problems then you might also try running Windows' built-in System File Checker... Go to a run command and type:
sfc /scannow
This process will scan and replace/fix damaged/missing Windows system files. Try and and see if your problem goes away.
If those two options don't work then try the repair install that Spyordie007 suggested...
Eps.