I notice that many people use seo spyglass for link analysis. I think it's the only tool to report on links that are currently in place. The problem with many other tools is that they just grab links from their index without checking them for relevancy. As a result, the amount of links reported on is overwhelming but how useful they are without a relevancy check? Spyglass is different. It finds relevant links only. It analyzes each link across many factors, including anchor text, google pr, alexa rank, number of external links on this pages and lots of other stuff. The tool allows you to update backlink data over time.
So thus I believe spyglass offers a more complete analysis.