If your Windows system ever blows a gasket, you try everything and it's still not working correctly, it'll probably have to be reinstalled.  This is why image file backup systems are so great.  Five minutes rewriting the system and you're good to go.

You can try reinstalling Windows over the present system, but don't be surprised if it creates more problems than it solves.  Your current programs aren't going to like Windows coming along and rewriting configuration files and the like.  In the long run, it would be better just to bite the bullet, reinstall Windows, then take the time to reinstall your apps.
 

The Process

The actual procedure is fairly simple.  Boot from the install disc, click a few buttons, that's it.  The most complicated thing you'll have to do is select the proper time zone.

All three versions of Windows give you the option of which partition you want to install it on.  99% of the time that would be the C Drive.  All three versions give you the option to format the partition first, which you should do.

It should go without saying that (assuming your present system is still running) you should first back up everything to a separate partition.  For programs that have custom settings, address books, templates, etc, you'll want to fire up the program and see if there's a way to export the data files.  You can save your Favorites in Internet Explorer, your email program should have both a way to export the emails and the address book, and any kind of spreadsheet program like Excel will have a way to export its database.  There's extended info on my backup site.

In other cases, like if you wanted to save the high scores from some game, you'd have to dig up the data file manually.  So, if you're dealing with important addresses and the like, either double-check that it's exporting the database (or you're saving the right file), or just make a copy of the whole program folder so you can paw through it later.  In many cases, after you install the program again, you can just overwrite it with the saved program and whatever settings it had saved should be in play.

It's also important to note that some programs store their info in the Registry and it's going to be lost with the new install.  If it's important, you can always put the old version's image file back in the system and boot up from it and grab the info, then put the new system back in and re-enter the data manually.
 

You should also make sure you have all the install disks for your peripheral hardware.  This includes your video card, audio card, modem, printer and scanner.  Most likely any ROM drives will be recognized by Windows.  It might also recognize some of your other devices, such as the printer or scanner, but you'll need to install the manufacturer's software to the get extra features, like "remaining ink".

Almost all installation programs and/or drivers can be found on the manufacturers' Web sites.  If/when you find the manufacturer's site, look for a "Support", "Drivers" or "Downloads" area.
 

Windows Installation

Okay, ready?  Remember, we're going to wipe the C Drive clean, so be sure everything you want to save is on a different drive.  You'll also need the Windows registration number handy.  It's on the sticker on the original jewel box.

Slap the installation disc in the drive and reboot.  You should see a "Press any key to boot from disc" message.  If you don't:

You'll need to adjust the BIOS.  Reboot and hold down whichever key the screen says to use (usually the F2, F10 or Delete key) to access the BIOS.  There should be a 'BOOT' area, at which point you should see some kind of "boot order", in which case you want the ROM drive to be first.  You usually use the arrow keys to scoot around, the Enter key to enter areas, and often the Page Up and Page Down keys to shuffle items around.  ESC usually brings you back up a level, slide across to the Exit Menu to save the settings and reboot.

Once the disc boots, just follow the on-screen instructions.  If you have an existing Windows on the drive, have the install program 'Quick format' the drive first.  Use "FAT32" (if given the option) unless you specifically want "NTFS", but it doesn't ultimately matter.

After the dust settles, be sure to go through the Setup page, and check out the 'Organize' page before you start installing your apps.