Mendeley allows you to make notes and annotate PDFs as you read them.
To open up a PDF document in Mendeley, either double-click on a reference that is linked to a PDF in the main document window, or, once a reference has already been selected, click on the PDF file as it appears in the Details pane on the right.
To highlight sections in your PDF document, click on the Highlight icon in the toolbar and select the desired text.
To add a note to a PDF document, click on the Note icon in the toolbar, then click on the spot within the PDF, and type your note.