Almost all windows programs place data in places that cause an OS slowdown. Many also run all the time, or have "quicklaunchers" that load part of the program in ram, so that it starts faster, but slows the system down. Lifehacker has linked an interesting article testing the effects of a number of different, popular programs, so if your computer is slow and you know spyware isn't a problem (a difficult assumption to make) take a look at this article.
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