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<div id="container">
<div id="header" />
<div id="content" />
<div id="nav" />
<div id="footer" />
</div>
I don't see anything wrong here at all. It's very logical and helps with styling later on.
I rarely use spans, but there is use for them too. For example, I want to style all numbers on the page differently. Or sometimes a certain word/phrase needs to be visually emphasised, but has not semantic emphasis, best way to do that is to use span.