A general purpose application that I use for my games is Zim. Zim defines itself as a desktop wiki editor. It is a general purpose tree text editor, perfectly fitted to brainstorming your ideas or organizing plots, setting, ideas or anything. From the web page:
Zim aims to bring the concept of a wiki to your desktop. Every page
is saved as a text file with wiki markup. Pages can contain links to
other pages, and are saved automatically. Creating a new page is as
easy as linking to a non-existing page. This tool is intended to keep
track of TODO lists or to serve as a personal scratch book. But it
will also serve you when writing longer and more complicated
A "desktop wiki" means that we try to capture the idea of a wiki, not
as a webpage but as a collection of files on your local file system
that can be edited with a GUI application. The main focus is a kind of
personal wiki that serves for all kind of notes: todo-lists,
addresses, brainstorm ideas etc.
But we want to go further then just a wiki filled with random content.
It should also be possible to use you random notes as the basis for
more structured data: articles, presentations etc. Zim will not
include tools to layout a presentation or something like that, you
should use your office suite of choice for that, but it should be a
tool that can deliver all the content for a presentation in a form
that only needs a template and some layout before usage. Therefore
certain features normally not found in wikis will be added.
The tree organization allows me to easily organize plots, subplots, scenes inside the subplots, or notes to the scenes. I can link a scene with the characters that appear on it.
Zim has lot of plugins that extend its functionality, but, as any general purpose applications, Zim lacks many of Masterplan's features. The big advantage for me is the speed at which you work with it.
Like all the tools I use, Zim is free as in freedom and as in beer.
Another free general purpose tool that could be used for that purpose could be Freemind. I don't use it, but I have seen a friend organizing his work notes on it, and can be used to quick brainstorming and to draw flow charts.
OpenRPG was primarily aimed to online playing, but I recall using it to organize adventure data. Many, many years have passed from that, so I don't remember it very well, and I don't know its current status, but I include it in the answer for if you want to look for it.