Having a relevant website theme is probably the most important methodology for search engine relevancy. A website theme is a site wide focusing around your keyword topics. One factor to look out for is dilution of theme. This is when you site talks about too many different types of topics or themes. To avoid this you should always develop your site around a similar range of keyword topics.
If your site already has a bunch of unfocused diluting content then you will want to separate that content into themed areas or directories. This way you will be able to strengthen each core theme so the engines won't see your whole site as a grouping of too many themes, rather it will see a large resource site with separate areas of strong focused content.
If you site has similar themes but still seems to be diluting the overall site then you might want cross link these themes while still keeping them in separate directories. This way you can create a general site theme while still keeping the broad unfocused content grouped to avoid dilution.
Other areas of website theme focusing would be to make sure you use keyword relevant anchor text on internal text linking. Simply make sure the link text has keywords that are on the page the link is pointing to. Never use keywords in the anchor text if the page you are pointing to doesn't even talk about the terms. This would create theme dilution and would weaken the page you are pointing too.
Just don't talk about to many topics on one site without grouping the content by theme. Keep everything clear and sorted.
The Full Search Relevancy Philosophy