Earlier this week, a co-worker let me know about a tool aimed at helping people write branching story lines, mainly for games. It's called Articy:draft and allows you to define the flow of your story, the conversations (even handles multiple-choice dialogue systems). You can also create annotated maps of the various locations. It's multi-user and integrates with version control systems. It looks really cool, but the benefits/price ratio will make it hard to convince anyone to buy licences.
Regardless, it's worth checking it out: