Evernote Premium subscribers can insert and annotate PDFs in notes.
Evernote allows you to conveniently insert PDFs into notes with drag-and-drop, and recently added support for annotating PDFs. Currently, this feature is only available for premium subscribers of Evernote.
The advantages of keeping your PDFs in Evernote are:
you can search across all your PDFs and annotations using the search box;
you can organize your PDFs using Evernote's notebooks and tags; and
you can keep PDF content together with text and audio in the same note, which is useful for attaching a short summary of the PDF.
Evernote provides a handy "annotation summary" option which pulls out all your annotations from the PDF and attaches it visually to the beginning of the PDF. This feature can be turned off at any point.
Text annotations in Evernote (shown as red text with white outlines in the screenshot) have more visual weight than text annotations made in Preview or other PDF editing apps, which makes it easier to review.
Unfortunately, Evernote doesn't support table of contents (TOC) in PDFs so you have to scroll through long PDFs. To work around this problem, you may prefer to embed shorter PDFs of 20-40 pages at a time. You can select a range of pages in Preview's thumbnail pane and drag it into Evernote, or use PDFExplode to separate a long PDF into logical chapters based on the TOC.
Evernote provides an annotation summary for the PDF and also shows useful context around the annotation.