IMO, it's still worth it... only thing I can think of that it may mess up are some p2p filesharing proggies that freak out once they realize you've removed the ad-/spy-ware they installed.
Btw, I think the next Gator-popup after running Ad-Aware or Spybot will claim that "the force is strong in you" and ask you to join the dark side.
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I want a hippo.
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