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)

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,

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 disk clean up tools and registry scrubbing tools are conservative, they don't clean as much as they might; they err on the side of leaving items intact in case you need them, because that's better than breaking your machine entirely eg making it unbootable.

If you want to really see the difference, export the registry to a file and use WinMerge or similar to compare the registry from the machine in its two different states.

You can do the same thing with the file system, dir . /s >> textfile.txt to make a file with all the filenames in it.

Also there's the issue of drivers, when you reinstall you will get the default windows drivers, maybe you had a bad driver previously. That can make a big difference, for example, you can get the CD or HDD into PIO mode instead of UDMA mode by mistake or bad drivers, and that would affect it badly.

Don't forget that malware is good at hiding, so you might have had a virus or rootkit that is virtually undetectable, but takes up system resources.

A program that can defrag the pagefile and other files locked by Windows when it is running is PageDfrg."

"The short answer is that no matter how much time you spend ""cleaning"" out Windows, it's still going to be faster to format & reinstall everything. It'll be a huge turning point when this is no longer the case.

On the bright side, I just plan on a reformat every 2-3 years, and use the time I'd otherwise be spending on registry scrubbing, etc. toward automating my reinstall process. (scripting, answer files, etc.)"

"To answer your question, to make everything perfect again.

To add to the things to do before such drastic measures:

Use Revo Uninstaller (when you
uninstall something) to minimise
registry files left behind.
Use Glary Utilities and Eusing
registry cleaner.
When you do reinstall, get things
(programs, settings, ...) as you want
them and make a drive image (for
example with Drive XML). When your computer is getting slow and glitchy, revert back to this image rather than reinstalling. That'll be a chunk quicker.

You could also remake your registry with a file from Black Viper's site or http://www.speedyvista.com/registry.php Haven't tried this myself but it might help."