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Can you do that? Can you describe content of your entire site in two words?
If not, you need to begin rethinking focus of your site. You might consider splitting your site into separate sites. Using same look and feel for each site, only different domains for different categories of your site. In this way, your visitors will still feel as if they are on same site, but engines will see different sites, each with their own "theme".
If you can describe focus of your site in two or three words your already well on your way to having a very themes friendly site.
The next step should be your homepage. The homepage of your site should focus on overall, two word theme of your site. The same two words you used to describe your site. These should be focus of your homepage.
All of subpages on your site, should focus on a narrower version of same theme you targeted on your homepage using an extension of same two word description of your site. If your two word description was "computer hardware", then your subpages should focus on keyphrases such as "ibm computer hardware", "toshiba computer hardware" etc.
The key is to always have same two word description as part of focus of your subpages. This keeps overall theme of site pure and focused, and easily picked up by a visiting engine.
A good example of an implementation of this would be an electronics store. A smart owner of an online electronics store would give each section of his store its own domain name. This could include a domain specifically for cell phones, another for televisions, another for stereos, etc. In doing this, he could then focus individual pages within each domain on specific types of those devices.
Let's look at an example.
Primary domain - www.daves-electronics-store.com
cell phone domain - www.daves-cell-phones.com
cell phone subpages: nokia-cell-phones.html motorola-cell-phones.html ericcson-cell-phones.html etc.
stereo domain - www.daves-stereos.com
stereo subpages: panasonic-stereos.html aiwa-stereos.html sony-stereos.html etc.
televisions domain - www.daves-televisions.com
televisions subpages: toshiba-televisions.html big-screen-televisions.html sony-televisions.html etc.
As you can see buy using above technique you can focus overall theme of each web site. The cell phone portion of site may deal with different types of cell phones on each page, but overall theme is still "cell phones" because this phrase would be found on each and every page.
When dealing with a themes based engine, focus is key. If all other things are equal, site that is most focused around specific search term, will come up on top.
John Buchanan is the author of the book "The Insider's Guide to Dominating The Search Engines", and publisher of "The Search Engine Bulletin", a FREE monthly newsletter. Visit him at http://www.se-secrets.com for more information or to sign up for the newsletter.