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At PubCon, Matt Cutts from Google said during the panel discussion that the presence of a url between script tags was "an interesting piece of information". I think this is where the rumors are coming from as to what Google might do with regards to javascript links in the future.
Read into that what you want, because he didn't tell us anything concrete.
A navigational javascript menu with 50 links on a every page will even out any emphasis that the site owner would put with its regular links.
I would not be suprised they use the info for checking yet unspidered pages though.
For example a plain text exteranal link in a body text or as cited source on the bottom would/could be a link to be counted as vote for whatever algo IMO.
Thats how it used to work with any scientific publication before the www.