I'd like to recommend Marginnote - a pdf annotater and reader, I've recently discovered after a recommendation on Mac Power Users.
Marginnote allows you to import PDFs and enter highlights and annotations. Crucially, it organises the annotations and highlights into its own outliner / mindmapper. Now I've started using it i realise I could have done something similar with Keyboard maestro and ithoughtsX, but this is much more elegant.
Even better, it provides links to the highlights / annotations. So you can copy the URL into dynalist, and you now have a link to a specific part of a pdf. It is seamless and works brilliantly, even on ios (although on ios links from dynalist app to other apps doesn't work properly yet - see my bug report)
I've bought the iOS version and OS version, (there are free trials), the latter with a discount from imore. Over the past couple of weeks it has markedly improved my reading of pdfs for work.