Hypothesis (hypothes.is) is an annotating tool, comes as an extension for Chrome Web browser, which runs as an overlay on any webpage or pdf (opened inside Chrome) and allows you to highlight and annotate content with collaborative features.
For editing complex documents that contain headings, chapters, equations, formulae, inserting and managing citations & references, exporting to different journal formats, etc, etc. How about the collaboration abilities of multiple people editing the same document at the same time? Then you need this app.
Is it really possible to annotate a video? Annotate.tv offers a solution close to that. Annotate.tv provides an optimized note-taking flow from Youtube videos, especially with ease.