I'd recommend something like articy draft for the game concept, story, dialogs, well planning in general but it's quite an expensive program. http://www.nevigo.com/en/articydraft/overview/
- actually available on steam too for a slightly cheaper price I think?
Alternatively you could type up a gdd (game design document - or god damn document
, as I call it) which you will type out a general game plan - sort of a guideline of targets for you to stick to, or for refreshing your memory. http://www.gamepitches.com/game-designs/
- for some ideas. (actually some design documents for commercial games on there too)
there's a really nice flow chart (mind map) type program called yEd. it's free too & has loads of customizable options. It's really useful for organizing stuff into certain orders or for creating branches. http://www.yworks.com/en/products_yed_about.html
there's also chatmapper - it's like a basic version of articy draft that a lot of developers used before articy was released. fairly cheap I think - or free for non-profit games. http://www.chatmapper.com