BibDesk for filing (and of course as a citation manager). Any notes for an article I store as an identically named plain text file generated by text-to-speech dictation while I'm reading, e.g., "page 7, column 2, VERIFY they used 0 point 1 molar thiosulfate, but I believe that 0 point 5 would be necessary to reproduce their results". I rely on Spotlight to find things.