- Google Webmaster Tools shows your internal link counts to different pages. You can use that to show which pages are being emphasized on a crude level.
- Optispider ($129) shows on site link structure and compares link text to page titles
- SEO4Fun has a free PageRankBot tool which shows internal link flow. I think it is a bit complex to set up, but is cool when you get it set up.
- Track a few pages of your site with a tool like CrazyEgg to see what links users are clicking on and if you are drawing enough attention to the most important assets on your site.
- Use data from your web analytics tools to focus more link equity on your most important (highest traffic and best converting) pages
A few more advanced ideas
- If your site is large and you keep producing new content, use Google's date based filters to look for new pages that are of low quality / noisy (like a page dedicated to a photo but with no text on it, or other common duplicate content issues)
- Use analytics to track how many pages (and which pages) are pulling in traffic. Compare those pages with all the pages on your site to see if you can free up some dead weight, or if you have a valuable section of your site that is not well linked to. You can use Xenu Link Sleuth, a sitemap generator, or data from Google Webmaster Tools to see what pages are linked to (and perhaps getting indexed).
- If a particular page works well for you consider adding more content to that page to pick up a broader basket of related keywords. If a particular query works well for you consider creating a second page to target that query.
- If you have a high authority page that links out to many other websites consider adding more internal links to that page to keep more of the link flow internal.
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