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I personally like using iframes (my audiences are relatively small and narrowly targeted). It is more a matter, IMHO, of objective and personal preference. The iframes allow me to present a visual appearance more in tune with my objective.
I'd say it depends. I have a site that uses a combination of both. If you want the individual page to refresh (using a post or header()), it might be better to put in an IFRAME so that it does not interfere with the rest of the page. Just my $.02
I would argue strongly in favour of the different includes files. iframes are by no means a widely supported construct. Albeit they are supported by the most widely used browser, using iframes just screams proprietary. Use includes.
Real programmers don't comment their code. If it was hard to write, it should be hard to understand.