When you want to read and digest the content in a PDF thoroughly, PDFoo provides an efficient way to do so. The PDFoo app makes it possible to create a link to a specific location in the PDF, which allows you to focus on understanding the big picture while the details are just a click away.
Zengobi's Curio app has an amazing "lists" feature which allows you to position several list boxes on an infinite canvas (known as "idea space" in Curio.) If you select such a list box, and hit CMD+V to paste the clipboard contents, it gets automatically appended to the list. This makes it very convenient to use Curio with PDFoo: copy text from PDFoo, select a list box in Curio, and paste the content with a PDFoo URL appended to the text. The figure below shows a Curio idea space used to work through the OmniGraffle 6 user manual, and includes several "see also" links to detailed content in the PDF. In a similar manner, you can efficiently work through any important PDF using idea spaces in Curio and PDFoo copy-paste.