Use PDFoo to create links into a PDF - to chapters, to sections, to pages, and even point on a page. Arrange these links in a mindmap for quick lookups. In this example, the mindmap is created using Mindnode Pro (a excellent lightweight app with iCloud integration). Any application that supports rich text notes also supports PDFoo URLs - applications such as Evernote, Curio, DevonThink, NoteShare, Together, VoodooPad, Scrivener and more. You can even embed pdfoo URLs on a web page (such as a blog post or wiki page) and Safari will faithfully launch PDFoo upon request.

When you are editing the table of contents (TOC) manually in PDFOutliner, you have the option to either refer to pages using page labels (the numbers in red boxes on each page and below the thumbnails) or using the page numbers printed on each page. The video below shows how to use the "p" prefix for printed page numbers.