Site Structure - Internal Linking
Internal Linking isn't really an on-page factor as it has to do with other pages on your site linking to the page in question. Your internal links can have a huge impact on your search engine rankings when accompanied by good on-page optimization and proper external anchor text links.
The best way to think of Anchor text is to think of it as descriptive text. It should be descriptive of the page it points to. The more descriptive it is, the more optimized it is.
Anchor text, or Link text, are the visible words contained in a link. They are used to tell the search engines and your site visitors what they should expect to see on the next page if they click the link.
The problem is when you link to pages on your site with the link text being irrelevant. Some common examples are whn your link text is click here, read more, etc.
Links You Can't Optimize and Links You Can
There are some links that you just can't optimize without sacrificing usability and design. This is not a huge problem. The Home link at the top of the page should say home, as anything else would likely confuse a user.
All your navigation links should be for usability rather than SEO. If they can be optimized for both, that is great. If not, don't worry about it.
Where this comes into play is in the content section of your site. On the home page of this site, in the content section the link to the SEO guide is Real Estate SEO just like this one. It's not just SEO guide because that wouldn't be completely true as the guide is about SEO for real estate.
It's really important to use optimized link text wherever it makes sense.
Footer Links
Footer links are links that you can Optimize. But, the home page doesn't seem to get any boost for your keyword in most cases and is some cases it has been found to have a negative effect. This is likely because the search engines see it as trying to game the system.
It's also a good idea not to shove a rediculous amount of anchor text links into the footer and make it look all junky. If you going to throw a bunch of links in there it should look nice. Footers are for user experience as well as SEO. For some examples of good and bad footers go check out this post at seomoz.org: Footer Link Optimization for Search Engines and User Experience
A great place to get all your anchor text optimized links is in your sitemap. Your sitemap is a page that does nothing but link to other pages on your site with anchor text. If you don't have a sitmap you should make one and put a link to it in your footer.
Important Note: If you use optimized anchor text to point to a page on your site... The page it is pointing to should be optimized for that keyword phrase. See optimizing page copy
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