Many times we have been told here that the imperfect or non-standard HTML used in our websites won't affect SEO. I have just come across a piece written by Jennifer Kyrnin that suggests that this may not be the case and in fact she has stated that invalid HTML may hinder SEO?:
From Jennifer Kyrnin, your Guide to Web Design / HTML
The HTML tags that you use can affect your SEO. The first thing you should think about is that search engine robots are a lot like very simple Web browsers. Most of them can't view images, can't see Flash, and ignore any non-standard HTML. So when you're working on SEO the first thing you want to have is a page with valid HTML, valid CSS, and accessible HTML. Then you should worry about things like position of your content and HTML inside of frames.