PDF Annotation App?

Not sure if it will meet your needs (or if you already knew about it), but the built-in PDF viewer app Preview has annotation features via the Tools menu, both text on screen and notes, which can be viewed in a sidebar next to the document

 

Preview.app has good PDF annotation features, and saves the annotations back into the PDF.

Another popular & free app is Skim (http://skim-app.sourceforge.net/). One good reason to use Skim is that it doesn't modify the original PDF - which is great if you're storing your large PDFs in Dropbox & want your notes to sync fast. You can also export out your annotations to text. I recommend turning on the "Automatically save Skim notes backups" option in Preferences if you're storing in Dropbox. I also use Skim for its freehand annotations - connect a Wacom tablet & speed markup your way through a PDF, just like paper.

I wrote an app "PDFoo" ($3) for situations where you want to link to a particular page in a PDF. For example, the app can build URLs like pdfoo://aragon2013a/figure-13 to link to a particular figure or section in a research paper which you want to access quickly. I store my notes/commentary & these pdfoo URLs in Evernote/TextEdit/Devonthink/Mindnode etc. to build up searchable notes with links back to the PDF for context.