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In Windows, 1000 programs installed and 900 uninstalled is not the same as 100 programs installed. Meaning that if you're the sort of user (and I am) that installs and uninstalls a lot of programs to try them out, your registry is probably a bit of a mess.
At some point, I'd suggest you bite the bullet and repartition and reinstall. I recently did that after having my current installation for about 2 years and the resulting speed was amazing.
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