Wow, there are some seriously organised folks on here! Looking at all the spreadsheets and stuff you all use to keep track of things has convinced me that I'm definitely very happy just having a straight linear story with no branches! I'd love to be able to organise it and have all the wonderfully branching threads and stuff but I just don't think I could manage it, the thought alone makes my head hurt. That being said, I've got an idea for a story that would work really well with lots of threads/branches and I may give it a go. But it's second in the queue as my next project for Chyoa (a new story) is already underway.
I have to say that I actually like @pwizdelf 's story organizer a good deal, and with someone with as many chapters as I've written, and with what was lost to authors' views in going to CHYOA from CHYOO and CHYOO2, I am sorely tempted to cook something up that downloads my chapters and metadata into a big pile of Markdown snippets and an auxiliary database.
Honestly, if I was doing a complicated story, I would likely use some sort of planner to keep track of things. I recently went back and fixed a name in an older chapter of mine when I randomly noticed a mistake. (I was doing a new follow-up and as I looked at the previous chapter the mistake was glaringly obvious as I had just mixed up some names randomly.)