Positive effects of a OS re-install

Serverfault question ref: System degredation - does Windows slow down over time?

Mark Russinovich's take on The Case of the Slooooow System
describes how to analyze a slow system.

For personal experience, before a reinstall you could do these things...

Backup all data files (basically leave just the bare windows installation intact)

1. While I discuss the Windows boot partition; you could clean up the other drives similarly
   • Uninstall all unnecessary applications
   • Cleanup application caches
   • this would be browser caches and such
   • Use autoruns to check what starts with your system
   • take a call on what is required, stop or uninstall as you feel fit
   • Check if you can cleanup the Windows installation a bit more
   • Use RevoUninstaller to cleanup remaining bits
   • Use CCleaner to clean registry
   • Use JkDefrag and move all files to one end of the boot partition (option '-a 6')
   • Disable page file, reboot, re-enable page file to the maximum suggested size
   • use the custom setting to freeze the page file directly to that size
   • You could run JkDefrag once again with defaults ('-a 3'),
     if you feel like it after you restore your backed-up data files

Restore backed up data files.
Check the feel of the system for a couple of days.
You can always go ahead with the re-install/recovery if required after that.
Your data backup would already be in place.

I have used the PageDefrag and Contig tools referred by Molly in the other answer.
These are great tools. But, I have a few opinions,

1. It is not always useful to run Contig on multiple files of a partition
   • I have found JkDefrag options doing a better job (nothing against Contig here)
   • There are times when removing a Page file and creating a fixed size one in a defraged partition works better than PageDefrag (which cannot do much if your partition is nearly full to start with; again, not a problem of PageDefrag)
   • In the interests of keeping more free-space on the boot partition,
     you might consider moving the pagefile.sys file to another drive (not partition),
     It is suggested by some.

The biggest thing is the file system. Unfortunately, no matter how much you defrag, there are files that will not and can not be organised correctly. As a result, as the computer gets used more and more these files (like the registry, critical system files) grow larger and more fragmented, which leads to reduced performance.

Invalid registry keys are also a big performance problem. Although you've mentioned you cleaned the registry on a regular basis, you have no way to know that what you're doing is actually getting rid of all the invalid keys - unless you want to search through the registry by hand, you're relying on what the author of the tool deems to be invalid.

(That said, registry cleaners like CCleaner are awesome, even if they might miss stuff that I might remove)

Also, the file system can suffer corruption issues over time to - typically people do a format of some description when they reinstall, which replaces the file system, and typically any corruption that goes along with it.

Unfortunately, Windows is like a giant filing cabinet. You can do your best to keep it clean and organized, but eventually you're going to just have to rip your files out and start all over again.

Edit: Molly pointed out some fantastic tools in the comments that may help in defragmenting large system files that aren't normally defraggable (is that even a word) by a normal defrag tool. These tools if used properly, could help in prolonging that reformat.