I'm still looking for the perfect software to help me write D&D adventures, from brainstorming ideas to creating all the encounters in detail. I can't say I have found it yet. One thing I like is Evernote, not because it has the best structure, but because it stores my notes in the cloud, where they can be accessed via a PC client, via a browser, or via my iPad. Masterplan on the other hand is better designed for a story flowchart with encounters, but only works on one fixed PC unless you use mail to ship your files around.

An adventure isn't just a series of encounters, although that is what the final product resembles to most. But at the start there are various ideas for the plot, for NPCs, or for specific items or events you want to include. For the brainstorming phase of gathering all those ideas I just discovered an iOS app called Stickyboard 2. It allows me to put my ideas of virtual sticky notes, arrange those notes on a virtual white board, and to draw on that whiteboard. Useful for sorting ideas, but it doesn't go beyond that.

I've been looking into mind mapping or similar software to create some sort of graph or chart connecting all the various ideas for the adventure, but haven't been able to find one I like. Anybody got a recommendation?

For the final step, producing the finished adventure with all the details, I'm boringly using Word. Monsters are copied from the WotC official D&D Adventure Tools monster builder. And I use either poster maps I have available, or create my own with Campaign Cartographer 3. And I just ordered some Gamemastery Face Cards as illustrations for my NPCs.