Interesting question. I don't have a recommendation, but I've tracked my own thoughts in branching-tree format for a long time, by egregious abuse of indentation levels in a text editor...works for me, but you'd have to think there'd be a few better organizer programs out there. I know there's an old Win16 program that's sort of like this, but I'm damned if I can remember the name and anyway it wasn't very good.
If it came down to it, you could use a simple personal test server like QuickPHP coupled with a folder of simple HTML files...
