I use Twine too, whether or not I’m writing in Twine, just because it’s easy to create nodes that are labeled in a way that makes sense and move them around. It feels more intuitive than other branch-mapping tools I’ve tried.
If I have a game flow that depends a lot on items or puzzle solving, I also like using Puzzlon, though it’s a little more fiddly (I end up having to fix my own code mistakes a lot).