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We ran a student promotion a few years ago which got us mentioned on a lot of university sites which resulted in backlinks, so never had to.
The Edu links are varied, some just say "click here" or are anchored on the domain nameThese are exactly the types of links you should not worry about. In fact, you can save quite some time by disregarding these and instead going after those links that have three-four-five word phrases in the anchor that could be considered the phrases you were trying to rank for.
you *could* try changing the URLs of the pages that are linked to, which would instantly render those backlinks invalid.Nope. I played with this extensively (pre- and after-Penguin) trying to remedy the issue of bad links from WordPress themes I wrongheadedly sponsored back in 2009. 404-ing or 410-ing the link target URL does nothing to improve the ranking (or remove penalty) of the site overall.
So my question is why do some sites get penalized for them? What makes the difference?
the bad/good ratio is probably the most telling and easily computed one
if a design agency distributes a theme with a link in the footer, why isn't this link a legitimate "vote" for the agency's website? Why does it need to be nofollow? If many websites choose the theme, then the designer's website is surely worth checking out.
if a design agency distributes a theme with a link in the footer, why isn't this link a legitimate "vote" for the agency's website?