The last game I made, I used RPG Maker VX Ace! My next game will be made in RPG Maker MV, and I’ve got a couple of games that will be made using the Tyrano visual novel engine.
In terms of the art of these games, if I’m not buying already made assets, I’m making them myself in Aseprite, Pixelmator Pro, or Photoshop Elements.
For planning and progress and whatnot, I use a combination of Trello and GoodNotes. Trello I use to keep track of projects and GoodNotes I use for coming up with ideas, outlining plot points, etc.