I'm playing with Mendeley and ReadCube. I like how both let me collect, search, highlight & take notes (I tend to like the note taking on ReadCube better - I don't like the yellow quote bubble that you have to click on to read the notes). Both seem to have some issues as reference managers, though Mendeley seems to win here.
Any decided preferences? Other program suggestions?
ps Grahl pdf annotator served me well letting me write on the pdf if you have a tablet pc (but it's not free).