The Filtered HTML as an option "Spam link deterrent" that if enabled, "Drupal will add rel="nofollow" to all links, as a measure to reduce the effectiveness of spam links."
That should only be done to external links, not internal links. In SEO terms that can be confused with Page Rank Sculpting.
As Matt Cutts (Google) said (http://www.mattcutts.com/blog/pagerank-sculpting/):
Q: Does this mean “PageRank sculpting” (trying to change how PageRank flows within your site using e.g. nofollow) is a bad idea?
A: I wouldn’t recommend it, because it isn’t the most effective way to utilize your PageRank. In general, I would let PageRank flow freely within your site. The notion of “PageRank sculpting” has always been a second- or third-order recommendation for us. I would recommend the first-order things to pay attention to are 1) making great content that will attract links in the first place, and 2) choosing a site architecture that makes your site usable/crawlable for humans and search engines alike.
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jhedstromFeature -> 8.1.