Try a full reinstall of Windows. Your data directories will be unaffected and your Window settings kept.
If that does'nt work delete the Windows directories and system files (command.com etc) and then reinstall windows (You will have to do a reinstall of the applications though).
If that does'nt work you might want to take the oportunity of buying a new large 40 or 60Gb drive (now cheap(ish). Put in in as the master, install Windows and your applications. Put your present drive in as slave. Copy your data across and then reformat as a spare.
Utilities such as Norton Utilities can have some success in curing problems, but at %50 of the price of a new hard drive you have to decide which is the preferable option.