I thought a quick list of some of my tools might help others as well.
For general document management, Google Drive is the way to go.
When I’m early-stage brainstorming, trying to get my head around a problem, I find that I’m usually totally scatterbrained. I’ll see small issues and hound off trying to address them before pulling back to the big picture again and forgetting what I just fixed. I find that mind-mapping software helps immeasurably here, and the tool that is the best that I’ve found is MindMeister (horrifically awful name). It integrates with Google Drive, so all my mind maps show up in my Drive folder on my machine and are available on the web as well. They also have a mobile application so I can throw things into a mind map from my iPhone.
For UML modeling, which I use extensively—thus planting me in a solid minority, I know—I use UMLet. It is quick, dirty, ugly, fast, simple, and gets diagrams on and off the clipboard faster than any other tool and so ends up being a great collaboration tool even in email.
For editing, I’m an emacs user. Either you get it or you don’t.
I’m sure there’s more, but that’s a good start.