This article is part two of the series on optimizing Drupal.org for search engines.
Rel=nofollow is a microformat that when applied to links tells search engines, "I do not vouch for the quality of this link". It tells Google that the linking page does not vouch for the quality of the linked-to page.
Nofollow is used on Drupal.org to reduce the motivation of users to post spam. When the site is viewed with the Firefox Search Status Extension, the nofollowed links show up highlighted in pink, showing the extent of the issue:

The problem with nofollow on Drupal.org is that it is getting applied to internal links. So pages that are important and that get linked to often are not getting the search engine "link juice" that they should.
One solution would be to apply a "nofollow whitelist" to the Input Filter on Drupal.org, so that pages from Drupal, its subdomains, and other official sites always have rel=nofollow removed from their links. That way nodes that are important and that get linked to often by webmasters and users would start to get more link juice and be seen as more important by search engines. That would include the often referenced pages like the excellent Drupal Handbooks.
Drupal.org has so much link popularity (PageRank 9) that it could rank #1 for just about any Drupal term that it is optimized for. One important factor is to make sure that the relevant keywords appear in the <title> elements, the <h1> elements, and in the body text. I'll use the Drupal Handbooks as an example. The Drupal Handbooks contain some of the best Drupal tutorials on the Web, yet the Handbooks do not rank in Google for those keywords.
If you search Google for drupal tutorials Drupal.org is only #7 and #8, and the pages listed are just forum threads—not the main tutorial section, the Drupal Handbooks.
Search engine visitors are more likely to search for the keywords drupal tutorials than drupal handbooks. Some of the best Drupal tutorials are found in the Drupal handbook pages, and it would be appropriate for Google to have the Drupal handbooks at #1 for the keywords drupal tutorials.
On the page http://drupal.org/handbooks, I would change to title element from:
<title>Drupal handbooks | drupal.org</title>
to
<title>Drupal handbooks and tutorials | drupal.org</title>
I would also change the H1 element of that page to <h1>Drupal Handbooks and Tutorials</h1>. Currently the H1 element is just <h1>Drupal Handbooks</h1> as shown in the image below:

This is Part Two in a series on SEO recommendations for Drupal.org. Part One can be found here. Part Three covers duplicate content issues.