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Are you talking about links in the footer? In the sidebar? Navigation? Or content? When you're talking site-wide links in general, you only want links that make sense to have sitewide (for example: your homepage, about us page, contact page etc.), and you don't want to use anchor text that manipulates relevancy - if you're linking to your homepage, it makes sense for the anchor text to be "home", and I don't think you'd be penalized for that. It's worth checking out Rand's recent over-optimization whiteboard friday though - there was some very good info in there regarding site-wide links.