I don't know what it is with the others here, I haven't met someone that doesn't know what you are talking about. There are many reasons for it, but some have not been identified.
I'll start with a better description for those that don't know. A fresh install of Windows will boot in under 1min. Over a period of 6 months the computer's boot time will not only slow but the entire experience of the OS is not on par with a clean slate. If you ever reinstall windows after 1 year of use you are sure to see the difference.
Reasons for the slow down have been attributed to increased clutter in your registry, and fragmentation of your disk. You have noticed that uninstalling does not help, this is in part because everything isn't cleaned from the registry. Ad-ware can be an issue, but this is usually not the cause.
You can get registry cleaners, defreg, and remove ad-ware, but even this will not return the system to its original speed, no one has come up with a reasonable explanation for this, it just is.
Note to others, this is not a normal behavior for an OS that is being used, I have been using Linux for 4 years, while this wasn't without re-installation, there had never been performance increase from a re-install or a slowdown from large amounts of installing/uninstalling programs.