I have recently discovered Papers, a beautiful software package for Mac to organise my scientific papers: absolute heaven! I used to have lots of folders with downloaded pdf's, named by subject and numbered according to my Endnote libraries so I could keep track of them, but of course I could never find anything in the end.
I am now in the process of importing all of these scattered pdf's into one large Papers library. For an obsessively organised person like me, this process itself is already utter joy: I drag the pdf into Papers, click "match" and the programme then finds the metadata, places it in the library, and renames the pdf according to a standardised format. It all looks so neat! Oh, and it makes a really funky sound after a successful match :-)
So now they're all together, I can organise my papers further into (smart) collections, tag them, mark them read/unread, flag them, etc. And I can still use Endnote for my bibliographies, which, for the time being at least, is needed for the work in progress. Basically, you can export any selection of Papers to an Endnote XML file (select "Endnote 8 or higher"), and then import into an Endnote library (be sure to select "Endnote Generated XML"). After having set the temporary delimiters to curly brackets in the Preferences section, you can then use Papers (or Endnote) to copy the selected papers as (Shift Command E) an Endnote citation into your text editor.