GB Studio is awesome, it's really easy to pick up, with no programming experience needed and you can get a game up and running really fast ON A REAL GAMEBOY!
Palette Wizard is a great place to start when deciding on the looks of your game, it allows you to easily craft palettes and edit them to fit your needs.
This tool allows you to create incredible 3D models by doing voxel art, and it looks so cute and pixelated that it gives that retro vibe.
It allows you to animate, try different color palettes and then export to spritesheets, split into layers and so much more.
This tool is great when you are designing your new tileset, it allows you to easily go from one tile to all the different combinations you need to make.
Not only that but it also has smart brushes so that you can try your tileset in a very nice tile map editor.
AssetForge is the ultimate 3D prototyping tool, it comes with a bunch of base models you can drag and move around, easily transform them to create your own complex models.
It was made by Kenney Studio and if you know "asset jesus" then you know what to expect.
I found Dialogue Designer to be a good way to create dialogue trees for visual novels and history driven RPGs, the export format and the UI are both very friendly and accessible to writers, cause we all know that not everyone in a team is a programmer.
Pixel FX Designer is one of my favorite tools when designing special effects for pixel art games, it allows you to easily craft particle effects, and bake them into textures guaranteeing that they fit your palette and size restrictions.