There are plenty of note managers for Mac so it can be difficult to separate one from the other. Paperclip can associate notes to any application.
This discreet little program works by creating Stickies-style notes, onto which you can jot down pretty much anything and attach to a document or application. You can add more than just notes and even include links, pictures or videos. Via the preferences menu you can also choose between nine different bright Stickies colors.
Paperclip works with almost anything but you can also choose to specifically exclude applications but just adding them to the list in the preferences. Paperclip also offers a note viewer, which includes a search box, from which you can browse and find all similar notes or quickly look for a specific one.
Paperclip can be a little unstable, but don't forget that it's only been recently released.
A simple and sober note taker, Paperclip can associate 'Stickies' to any document or application.