I was wondering if Search Engine spiders can see the comments, when I open the source of the page the comments are not showing up (same as with disqus), so I’m assuming when the search engines crawl the page they won’t see the comments either? Is this assumption correct? If so, is there a way to change this?
Found the solution:
http://developers.facebook.com/docs/reference/plugins/comments/
How can I get an SEO boost from the comments left on my site?
The Facebook comments box is rendered in an iframe on your page, and
most search engines will not crawl content within an iframe. However,
you can access all the comments left on your site via the graph API as
described above. Simply grab the comments from the API and render them
in the body of your page behind the comments box. We recommend you
cache the results, as pulling the comments from the graph API on each
page load could slow down the rendering time of the page.
Only what get thrown to a crawl engine the crawl engine can see, hence these comments should be outputted in able to get crawled and saved into the SE database or whatever it uses to collect data about websites, you might check the headers the connection request came from, if it belongs to a crawl engine and that’s called a user agent in our case humans (browsers), here you can find a way to detect crawlers using PHP, after detecting it you force the comments to be shown in order to get crawled, here also a good resource on how to deal with crawlers from Google itself.
Now if you’re talking about Facebook comments, it’s impossible to let them indexed by the crawler or SE, when a crawler attempt to visit one of the Facebook pages it won’t be able to see users’ data because of the login page, and if you are talking about Facebook plugins you may do what what I suggested above, article talking about Facebook comments crawling.