I use Papers (http://www.papersapp.com/ http://www.papersapp.com/) and DevonThink (http://www.devontechnologies.com/products/devonthink/overview.html http://www

I use Papers (http://www.papersapp.com/ http://www.papersapp.com/) and DevonThink (http://www.devontechnologies.com/products/devonthink/overview.html http://www.devontechnologies.com/products/devonthink/overvie...). The latter holds my notes, highlights and every piece of information I find somewhere; it can do basically any format, not just PDFs. Additionally it links them up with other things in your database (https://static1.squarespace.com/static/544bf5dae4b0dd27d7018fa8/t/55acedcfe4b0b14a3f0ff0ba/1437396435522/ https://static1.squarespace.com/static/544bf5dae4b0dd27d7018...). This plus the superior search makes retrieval a lot easier than in any other application I have found so far.