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My thoughts are that it is therefore better to place navigational items (e.g. the category menu) to the right instead of the left and therefore towards the bottom of the html?
Another benefit for wide pages that might get printed is that the nav gets cut off instead of the page content. It's very annoying to try to print something that goes wider than about 600 that has the nav on the left. The content gets cutoff and you're left with the nav.
I agree that it's generally better on the left in terms of readability, so I guess it really depends on your objectives. There are tradeoffs that need to be addressed before finalizing the design.
I've dabbled with this a little and used the following sites for reference:
You can then use "printer friendly" pages for your ecommerce site using the same pages with a different stylesheet.
I found it quite difficult to get to grips with the css positioning and all the different "hacks" needed for the various browsers, but it was quite good fun learning.
However the end result was that I could a have a left and right column on a page but have all the relevant body text at the top of the source code. Nice and easy for the robots.
Hope this helps a little.
As for left and right menu's, why not provide alternative CSS? even let users pick which ever side is most comfortable, store that in a cookie or something. For some things I like left, for others, right. Just whatever fits best on a particular page. Mine are mostly to the right, works well if you put good space around them.
print-friendly versions of pages are a great idea, whether you use CSS or Table-based layout, and fairly easy to code up, too.
finally, I suspect prominence in body text is less important than many folks imagine. stuff way down some of my big pages turns up unexpectedly in google refers. Google likes content. Don't we all.