Sure, you can backup files to another drive, external drive etc with a bootable utilities disk or a DVD based Linux distro. Copy your files over, re-partition and format your drive and re-install the OS. The only problem is that you will still need to re-install all your applications manually from their CD's.
What Hidream suggests can work only IF your original HDD structure had one separate Partition for the OS, and another for all your apps and data. Many people set up such a structure specifically to deal with OP's type of trouble. Then you CAN re-install the OS in the system-only Partition without disturbing (and losing) the stuff on the other Partition(s).
BUT this only works if the structure was set up ahead of time. If it was, be aware that any other info on that system Partition (e.g., app software) will be destroyed and need to be re-installed. You could also have to re-install app software anyway, because the re-install of the OS will create a new Registry that does not know about stuff already on other Partitions.
If you do NOT have that structure already established, do what canadian69 recommended. Back up all of your drive to an external device first. THEN go to work. You probably will have to re-install everything, then copy back from the backup all your data files. But before trying that, you could try something less drastic. Try using the original Windows Install CD to do a REPAIR INSTALL (NOT a normal full Install) just in case you're lucky enough to succeed. This process attempts to detect and replace any system files on the existing OS that are corrupted or lost, so it MAY solve your problem, depending on just how badly manged your OS is.