The choice here is going to be very much subjective and individual choice/ preference.
I tried StickyBrain 3.x and Circus Ponies Notebook, but settled on DevonTHink 1.9x.
DevonThink seemed to be able to handle large data sets much faster and easier. (I seemed to have dumped large amounts of data in there.) For a more modest use (not very large data sets which seemed to slow it down considerably), StickyBrain 3.x seemed quite useful.
You might want to try demos of all products and make your own choice, which is what I did. I think Applelinks had a review of this type of software comparing the various programs pro and con.
MLJ_osxcom