Robert_Charlton - 7:09 pm on Sep 2, 2010 (gmt 0)
A major thing I noticed in investigating the crash was that internal link size more than doubled in the wake of the redesign. Part of the jump was caused by going from a static, image-only top navigation section to a CSS-driven text link top nav with primary links going across the top, groups of secondary links dropping down on hover, and even tertiary links popping to the side when hovering over secondary links.
IMO, too many links on the home page can be a disaster... changing a logically organized navigation hierarchy into a situation with so many links on home that your important links are de-emphasized, and also confusing what the home page is about for the engines (and, I should add, for users).
Re nofollowing links, I wouldn't recommend this as a way to sculpt PageRank. Too many recent discussions even to cite one.