Skim (Mac OS only) is what Adobe Acrobat wants to be when it grows up, at least as a reading and annotation tool. While Acrobat Pro is hard to beat for OCR, PDF creation and optimization, it falls short in the realm of note-taking and annotation.
Stage in my thought process: One (Information Gathering)
Where I use it: Reading books and articles for research, including those digitized from the photography process.
What goes in it: My annotations on important sections in academic publications.
Why I chose it: Skim’s primary purpose is note-taking. Acrobat has note-taking options, but that’s not its primary goal, and the interface difference makes that very clear. Skim offers several different colors of highlighting, easy annotation, sticky notes, export formats and a number of search and filter features on notes that make it a clear winner.