Three great tools for backlink analysis have been constantly improving over the last few years. Open Site Explorer from SEOmoz, Ahrefs and Majestic SEO each have features that set them apart. This infographic from the folks at TechWyse tries to capture a general overview of fairly central aspects.
Other people have done some detailed analysis and discussion along the same lines. At the end of the day, it is best to spend time working with each of these tools to see which works best for your purposes.