The RPG Maker series is a good tool for creating a game, but even the makers can’t do everything. And especially when you plan to make a bigger or more complex game, then you will need tools to help and to organise everything.
Other users already have made lists of programs for certain areas - you can find them on the forum, and I’ll link them here later.
But I’ll begin with my own lists of tools I have used or plan to use/test in the future.
World/Story building tools:
Random Inn/Tavern Generator (including Menu, Rumors, List of Staff and Patrons, Website)
donjon; RPG Tools (Name, Quest, … Generation, Website)
Data organisation tools
Articy:Draft 14-day-Trial (professional story organisation including simulated storyflow)
Treepad: Personal Information Manager, Notes Organizer, Word Processor, PIM, Database and more! (Windows and Linux programs)
Organize anything, together. | Trello (webbased organisator, team organisation possible)
Game design articles
The Forge :: System Does Matter (one of several articles on the old Forge forum
I Have No Words & I Must Design