Papers looks interesting, but doesn't seem to quite do what I need. As a way to organize PDFs, it looks good, but as a way to organize
my notes in PDFs, I'm not seeing what I need.
Zotero looks more interesting. I don't care if the notes are stored in the PDF itself, but it looks like Zotero isn't yet able to look within a PDF and take bibliographical information or selected text from there. I guess I'd have to convert my existing PDF files to some other format, which would be somewhat of a nuisance.
What I need is something that replaces the "index card" method of reading, where you create a database of quotes or references, including citation, while reading, then organize those and use them to write afterward. For example, I'll need to write at least one literature review in the next couple of months. As I read through multiple documents, I need to be able to note interesting areas in each and categorize them. Then I need to be able to pull up that list of notes.
It looks to me like Zotero can do some of this this, but the lack of PDF support may be a critical failure. I was also hoping to be able to do it on the iLiad, but the full version of Firefox doesn't run there.