What is the best tool for determining the number of backlinks you have? I ask because I have several good do follow links that aren't showing up in the current tools I use, any idea why this is? Thanks in advance for the help.
You can check it manually by using link:yoururl this will return number of backlinks of your site on that search engine.
If you want a report from Yahoo Site Explorer providing the anchor text, page title, page header, whether it is no follow or not, and more try this backlink analysis tool. (copy / paste table to Excel)