Writer's Fallout Shelter

Personally, I use a notebook and a spreadsheet.

The notebook is to capture ideas as they occur, jot down research facts, things I need to look up, write down points I need to cover in a scene or section, and to rough out problematic areas.

The spreadsheet, I've discovered, is rather unique to me. The way I use it combines storyboarding (as I understand the concept) with notecards. Many members of my writing group uses notecards. The write one, maybe two sentences, describing a scene on a notecard and then they can spread them out on the table or tape them to the wall and organize them sequentially, moving them about as needed. Each member that uses notecards also uses notebooks.

Or was that not what you were after?