Aeon Timeline - A software that's all about making a timeline of what's going on in a story and which characters are present at each event. The software started as a genealogy software which means it has a lot of features that are wonderful for writing a story since a story emulates life. Just one example of how useful this tool is; if you put in the birthday of your characters then it will calculate how old they are during a particular event! Think about the math you're saving yourself!
4thewords - I've been having a major resurgence in gaming, which has distracted from my writing. But there is one known way to distract from a game, and that's by having another game. 4thewords is a writing related video game, where you have to defeat monsters by writing a certain amount of words in a time limit. Boss monsters get defeated by writing more words. While the concept is kinda simple it's just enough motivation to sit down and keep writing, let alone the fact that they have a streak counter which I've always found to be a great motivator! If I'm at day 100 there's no way I won't get in at least 150 words!
There are also the classics, which never age out!
Scrivner - Make flash cards that attach to your scenes. It makes it easy to look at the summery of your novel and rearrange as quick as a flash!
Google Doc's - This deserves an honorable mention, I don't like it as much for writing but for the editing it's wonderful! It makes it particularly easy for sharing one document with multiple people who can then comment on it. Everyone can see everyone else's comments and respond to them if they particularly disagree. The discourse can be one of the most valuable parts of the beta reading comments.
100 Squats per Day
Read 52 Books