Skim: PDF annotation, notetaking, highlighting

Skim allows you to annotate, highlight, and bookmark PDFs, then export your notes and highlights to text for further editing or present the annotated PDF with Powerpoint-like transitions. 

I use the exported Skim Notes file as a basis for writing my own summaries of long documents for reference and distribution. Skim-annotated PDFs can be flattened with embedded notes for reading by any PDF viewer, or retained in PDF-bundle format which allows further editing and annotation in Skim.

PDF Outliner Table of Contents and Outline creation for PDFs

Many PDFs don't take advantage of all the Table of contents, bookmarking or other internal navigation features available within Acrobat. For long articles, the lack of internal navigation can make it much more difficult to read and process. And sometimes it is helpful to create your own custom outline from a document. 

PDF Outliner makes it easy to create a Table of Contents or custom outline using a variety of automatic and manual methods, that permit annotation, custom linking within the document and custom formatting of the outline or TOC. 

Checkvist: outlining, notetaking

Checkvist is a web based outliner, checklist maker, hierarchical thinking assister, brain dump receptacle - with a very easy learning curve. I use it for outlining, starting to think about a project, capturing ideas. I don't use it for task management but it looks like it would be great for that too. Allows export to text and OPML, and there's an API for further integration.