Filters
The filters allows you to segment your link profile the way you find it useful to your analysis. You can create a variety of combinations that would wield important intelligence.
Tags
Tags are used to mark links that have a specific meaning to you. Starting from prospects and going to unnatural links the Tags are a great feature if you need to remember a set of links that you previously analyzed.
Other useful articles:
http://cognitiveseo.com/blog/3283/custom-backlink-filters-and-page-speed-improvements/
http://cognitiveseo.com/blog/2313/faster-link-prospecting-disavowing-tags-links/