Some people think that embedding a link to your site in a web product/plugin you distribute can lead to bad things, especially if it is not a nofollow link and your plugin is used by nefarious sites. http://www.jitbit.com/news/184-how-google-authorship-and-pen... has a bit about the Penguin algorithm and this effect.

Me neither :) But my line of thinking was that lots of sites that have nothing in common pointing to the same site... must mean that that site isn't isn't very relevant

(Now that I'm trying to explain it I see my mistake: it could just mean that the site is very general, like Facebook.)