For annotations and notes I love LiquidText (iOS only, http://liquidtext.net http://liquidtext.net). It’s great for ebooks and longer reviews, has a nice “accor

For annotations and notes I love LiquidText (iOS only, http://liquidtext.net http://liquidtext.net). It’s great for ebooks and longer reviews, has a nice “accordion” feature for comparing between distant pages, and can help produce nice summaries to share with others. File management is a pain, sufficient enough that I don’t use it for manuscripts. For those, I generally print them out and annotate directly. It’s really hard to beat paper. For organization, I use BibDesk (http://bibdesk.sourceforge.net http://bibdesk.sourceforge.net). I used Papers when it first came out, but for reasons relating to business practices I now forget I went back to BibDesk.