[samuraixp]

I use http://papersapp.com/ for handling PDF papers from arxiv.org etc.

It seems they have merged with readcube who want a yearly subscription however I was still able to buy a life time license to papers app a few months ago. I guess support will slowly disappear but for now its working great, with PDF sync via dropbox onto my iPad or iPhone, the ability to draw and take notes and search as well as download new papers. For your own PDFs I guess this would still work pretty well since you can search and annotate, create smart groups etc.