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I always remove the encoded footer and replace it with my own footer...encoded ANYTHING is shady to start with and there is no way to really know whats included in that crap...additionally some of the links are certainly not relevant to my content and that's probably not going to be beneficial to anyone's SEO.
As Fris said, some of them add stuff like phoning home to their server and that could very well come back to bite your sites up time and performance.
Now all that being said, I have included links to the authors or whoever on a separate generic "resource" type html page outside of my content to give credit..probably not what the author wants...but best I can do in most cases.
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