getting true layout and content seperation with (x)html and css is not possible. too much still depends on what order things occur in the html file. (at least, it's not possible while still maintaining compatibility with many browsers.)
and even some of the most modest graphic flourishes require stuffing things that aren't really content into your content.
i think you'd have to throw xslt into the mix to really get proper seperation all the way through. (or something like some php code pulling the real content
out of a database, and feeding it into an html+css layout.)
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I agree; besides, no matter how careful you are with the structure of your document you can't get around the fact that any navigation links have to be hard-coded in to every page on your site (at least as far as the HTML served up to the browser is concerned). Separating content from presentation using CSS in my opinion is something of a false ideal.
Instead, I use CSS to write semantically correct documnts. I get a huge kick out of the fact that I can put together a descriptive HTML document (with properly nested header elements, unordered lists, logical divisions and so forth) and use CSS to make it look how I want without having to put any purely presentational tags in to the markup. Other than documents being more accessible I don't know of any real benefits to this aproach at the moment, but I love the idea of a web full of semantically marked up XHTML documents just waiting to be explored by a new generation of "intelligent" user agents. And evne if that doesn't happen, it's still nice to know that I can write my own tools to extract semantic information from my documents at a later date (I'm already doing that with lecture notes I have typed up by extracting the header elements to create an outline of the documents - see here for a simple example).