I recently heard about Mendeley which turns out to be a useful reference tool and social network for researchers. Here you can add and organise all your pdfs, which you can annotate. The reference manager lets you generate citations and bibliographies.
I have also finally gotten round to downloading Evernote to have a play with. I think it’s great! You just highlight what you want to remember, click a button and it saves it. That works for text, pictures, documents, notes you write yourself. It’s easy to use and sleek to look at. It’s better than Mendeley for notes but doesn’t offer so much of the social aspect, so it depends what you need most: a pdf library stored somewhere or your own collection of all sorts of different things.
Both tools let you see your content on a number of devices that can be synced.