WordPress is a great SEO framework right out of the box. About the only thing you have to do is set the permalinks to a custom structure. One of the most popular permalink structure is /%postname%/, this will make the permalink http://www.domain.com/permalink/ compared to the original WordPress permalink which would be http://www.domain.com/?p=1.
WordPress also sets the slug (actual url link) to lowercase, and the title to proper case. So the link would be http://www.domain.com/custom-permalink/ and the Title (anchor text) would be Custom Permalink. Such as Custom Permalink
These are important elements to consider and should not be overlooked, especially on self designed sites.
I have 30+ sites that are money makers for me that are not built on any system. They are a homegrown design that I developed over the last few years to utilize affiliate links and make money. I have always used a permalink structure that matched what I used on WordPress sites, except for setting the case. So the one small change I have made recently is to make the slug all lowercase and the title anchor text proper case. This change has really helped. I am seeing a much more consistent indexing and search results.
If you have any homegrown developed sites I would highly recommend working on the permalink and slug structures.