I do use WordPress. To start, I wrote my own master theme framework that uses clean, minimal, pure, semantic and valid XHTML (even though it's served as HTML). That means using headings as they were intended, having the source code order defined (header, menu, content, sidebar, footer) to ensure that all pages that NEED to be are able to be indexed, using an actual image for my masthead (rather than abusing an H1 element), and so forth.
From there, I use the All In One SEO Pack to allow me to not only rewrite my page and post titles, but also write which keywords and meta descriptions I want to use on each page and post, rather than the whole blog (since hard-coding it n the header.php file will cause the same text to be used on every page and post).
I also use Enforce .www Preference as well to not only enforce whether or not I use the .www subdomain or not (I personally use it), but also to redirect all index.php calls to their directory (such as www.example.com/blog/index.php getting redirected to www.example.com/blog/).
The next thing I do is use Category Base Killer to remove the /category/ directory from many of the links - that way I don't have as many duplicate content issues since all the pages will have the same link structure.
Then I modify my robots.txt file to block the tags and archives sections from those spiders that actually obey the protocol (the legitimate spiders, of course, meaning search engine spiders). There's no need to block the category since /category/ has already been stripped from the URL string anyway, and the "articles" "entries" or whatever directory I have my blog posts in will be where the posts are at anyway (and they are where I want the engines to go to anyway). There are two ways you can do this. One is to use a hand-written robots.txt file; the other is to use KB robots.txt so you can manage your robots.txt file from within the Dashboard. I have a sneaky suspicion this feature may be incorporated into WordPress 2.5 (even though I haven't tried the betas) so keep your eyes peeled. If it does, then remove the plugin.
With regard to what ssandecki said, WordPress uses rel="nofollow" by default in comments, so there's no need to use a plugin to add it (or even modify the WordPress core files). But if you want to remove them, then the Do Follow plugin will let you do so.
You may also want to read Pushing WordPress's SEO Boundaries and WordPress SEO MasterClass For Competitive Niches, both by Andy Beard as well as Understanding Search Usability and Understanding Search Usability, Part 2 by Shari Thurow.
Chris, ToddW's blog is broken in Opera. I had to scroll down below the sidebar to read the content. It does appear to be obsolete in places though; other than that, I don't see a problem with what he wrote (especially since I like to use as few plugins as possible while getting the maximum gain out of what I do use).