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A common mistake is to use an iframe instead of an include for navigation. This makes it extremely hard for spiders to navigate around your site unless you have secondary navigation on your main page. You can still use iframes, but ensure you site works well without them. Don't forget also to provide alternative content for those with iframes disabled:
<iframe src="page.html" width="100" height="100">[b]<p>Alternative content here</p>[/b]</iframe>
When it comes to bot usability, what sort of methods can be done to get them to see links included in the iframe?
Can you have display:none, or visibility:hidden, and they will see it? What about z-indexed under the entire page, or in a really small font size at the bottom of the page or something...
<iframe src="page.html" width="100" height="100">
<p>Alternative <a href='page.html'>content here</a></p>
</iframe>
Now anything that doesn't support IFRAMES, including the spider, will see a link to the actual page. But for users that support it, they won't just the actual IFRAME.
<iframe src="page.html" width="100" height="100">
<p>Alternative <a href='page.html'>content here</a></p>
</iframe>
Be careful with this approach, spider will index page.html as a separate page. Search engine users directed to page.html will not find content useful unless it happens to be self contained and links back to rest of site, it probably will not have any navigation, banner, title tags etc.