The GameBook Authoring Tool: I use this to branch out my stories before writing them. You can write full-fledged CS game in them too, although I’m not sure about how good it would be.
Twine : Possibly the most well-known open-source tool out there. You can make full games in them (like this one), or you could just use them to simply branch your story out.
Chronicler: A project undertaken by @BenSeawalker, it’s pretty great for those who finds CS a bit difficult, and it can double as a branching tool as well.
Or you could go the old-fashioned way; MS Word and Paint flowcharts.
I’m pretty sure I missed a couple of these tools, so do your research before you jump right into them.