Unfortunately there's no one application that does it all. I use Google Docs for collaborative document editing with various teams I work with, Arena for collec

Unfortunately there's no one application that does it all. I use Google Docs for collaborative document editing with various teams I work with, Arena for collecting bookmarks, embeds, and images (some of that activity is collaborative), Evernote for collecting and synthesizing ideas (also sometimes collaborative), Trello for high-level project management, OmniFocus as a personal task manager / universal inbox for ideas, references, etc., and I was using Ulysses (and Daedelus for iPhone) as a kind of journal / space for thinking through ideas, but I'm slowly migrating that over to Evernote.