The structure of your site has a lot to do with how well you'll rank in the search engines. Now I'm not talking about HTML or any actual code, I'm talking about how your site is held together by its internal links. The navigation schemes you employ can drastically affect your ranking one way or the other and it is something that you absolutely must pay attention to if you want to make it to the top of the search engines.
The most important part of your site, more important than your actual content, is your menu. Yes, your menu is more important than your content. Why is this? Well without a usable menu a search engine may never find your content.
If you absolutely must use a menu that search engines cannot read you should include duplicate plain text menu somewhere on your page, or in noscript tags.
In addition to using normal HTML anchor tags you should put text, not images, in those tags. The reason is that the anchor text used to link to pages is a vital part of the ranking algorithm of many search engines, notably Google. So, if one of the pages on your site linked to from your menu is about "Golf" then linking to that page with the word "Golf" will fetch far greater a benefit that linking to that page with the picture of a golf ball.
Most menus also include a link to your home page with words like "Home" or "Index." If you're trying to optimize your index page this is a bad idea, you'll be much better off linking to your home page using text like "Keyword Home," the benefit from this one small change can be substantial.
So, building a search engine friendly menu is paramount to search engine success and populating that menu with keyword rich text links, including the link back to your homepage, can make a substantial difference in your ranking.