Pliny

Pliny is a tool that works with annotations or notes that you gather as you are reading - arguably the starting point for much personal scholarly research in the humanities. It can be used with both digital (web sites, images and PDF files) and non-digital (books, printed journal articles) materials. The text of the annotation can be anything that you wish to record - indeed, whatever strikes you about the material you are reading is fair game.
Pliny is designed assuming that you might well accumulate many notes (perhaps even thousands) over time, and that your note collection will then provide a base platform upon which you might develop some sort of interpretation of the materials they refer to. Thus, Pliny has components in it that go beyond annotation facilities to help you manage the notes and organise them, even if you have thousands of them to work through.
Get Pliny and take it for a spin to see how useful it can be for taking notes and making annotations.