yED & MindMaple lite are both nice free cloud / mind map type software. yED is 100% free. MindMaple lite is freeware version of the full software but it's nice enough - I preferred it over yED.
Having said that, the best program you can get is Articy Draft, but it's a bit pricey & I recommend buying it in a sale on steam if you can (it's usually cheaper if you buy it in a bundle with articy 2 dlc, I paid around €99 for it).
@ Damiano: I too use a board mounted above my desk, although mine is a whiteboard instead of a blackboard. Very useful for quickly jotting down notes - especially considering I only have to look up from my screen to see them.
P.S: articy draft has lots of export options to directly export your data into various game engines. Unfortunately VS is not one of them, but it does have support for condition switching, so you can prototype your scene layouts & various other things in it, besides writing your story / dialog scripts & organizing everything inside of a flow diagram - it does need a decent computer to run it though.