Twine is nice, and fun to write with. But I had the same problem as you, I always wanted to see my stories as I wrote them. Here are some gorgeous ones to inspire you: http://outspaced.fightingfantasy.org/SVG_Flowcharts/main.html - There’s all the fighting fantasy books there, as well as my favourite series, the Virtual Reality (which remind the most of Choice of Games).
I wrote a piece of software to help generate these kind of diagrams - try it out if you want, it’s free and at http://www.crumblyheadgames.co.uk/the-gamebook-authoring-tool/. It’s also rather new, and if you have any issues or ideas for it reply here or drop me an email 
If you don’t want to use it, but you are quite technical take a look at graphviz. http://www.graphviz.org/. It’s a great piece of open source/multi-platform software that lets you generate graphs/flow charts using a fairly logical scripting language.
Finally, you can do a web search for mind-mapping software. Organising your thoughts is a similar technique to writing a multi-choice book. You’ll find lots of options and I’m sure you’ll find something that fits the bill!
