I'm a big fan of the dropbox.com website. They have a footer full of links on the homepage, which is basically a minimalist site map that helps them avoid having a navigational header on the landing page.

Once you login, though, the footer basically goes away and is replaced with a small left-side, fixed "footer" that really contains non-task related links in a drop-up menu.

This seems like a very clean solution to the problems outlined in the article.