Ask HN: Windows applications to create/markup PDFs

Sorry if there is a generlized answer out here, but I am curious what you think.

I am looking for an applicatoin to create and markup PDFs in windows, preferable Open Source, but not a major requirement. I am a student, and prefer to type notes in org-mode or markdown if I can, but sometimes have to deal with PDFs, or sometimes it is easier to write out notes (I have a surface). I used onenote for a while, but have been pretty displeased with the way that it handles PDFs (Horribly slow syncing, files randomly disappearing, multiple apps). What tool would you use for taking notes on digital paper?