This list includes tools used by novice and professional game designers, particularly in the Indie Game realm. It includes game development engines, graphic design, and music/production. Additional tools are provided as well for storyboarding and for hard-core developers.
Game engines basically from least to most challenging. The less challenging items have more hand-holding that comes with reduced flexibility. The more challenging systems have a higher learning curve, but a lot more flexibility, especially when you get used to the scripting languages.
GameMaker Studio is good for prototyping games quickly, but has also been used to develop solid games thanks to its GameMaker Language scripting system. It is ideal for 2D platformers. Examples include Undertale and the AM2R Metroid 2 Remake that got cancelled before its time. It comes with an unlimited trial period to learn the ropes and a $31 dollar investment for the individual license to export to Mac and PC. Higher priced licenses allow exports to desktop, mobile, and even consoles.
RPG Maker MV is the latest iteration and can be used out of the box and/or customised with game art available on the website. It is ideal for making 2D RPG games (naturally). Scripting is made possible with Javascript and can export to many platforms. Indie games To The Moon and Rakuen were made with this engine. The standard license is $80 dollars and is available for all platforms through Steam.
Godot is a unique offering in that it is 100% free, including source code and can be used to make both 2D and 3D games. It uses a python-similar language called GDScript and is used in any educational institutions to teach how to make video games.
Unity is an extensible tool that allows the creation of basic game through existing processes or to utilize c# to make complex games, including some pretty big and famous titles out there. It specializes in 3D games, but can be used (with some overhead) to make 2D games as well. Indie sensation Monument Valley and the Steve Jackson Sorcery! games were made using Unity. The software starts out free to use, but gets progressively pricier depending on how much revenue your game makes and the features you want.
Game art tools, from simple to complex, general to specialized.
Pinta is a free raster editor based on Paint.net. It's no slouch though - the graphics in Stardew Valley were created entirely using Paint!
For those willing to spend some cash, Affinity Designer has very advanced tools for both vector and raster image design. At $50 dollars, non-recurring, it is cheaper than photoshop and gravit and has about the same, if not better, functionality!
This tool specializes in creating sprites, including animations for all the best 2D games. Goes well with your GameMaker Studio platformer or your RPG Maker creation.
This system can be used to easily edit both overhead maps and side-scroller levels with precision and accuracy. And best of all, it is totally free!
Blender is a free and opensource tool used for 3D graphics. Boundless tutorials exist for this program to help you get started. The graphics for Monument Valley were created in part using Blender.
A tool used to facilitate spritesheet building, it is free with limited functionality and unlocks for $40 dollars with a 50% indie discount for folks making under a limit with their games (or for those using it for fun). This turns tedious spritesheet building work into a breeze and integrates with many of the engines noted above.
Digital Audio Workstations from least to most expensive. All have a pretty steep learning curve but tutorials abound, both at the company sites and places like Udemy and YouTube.
Ardour is a hard-disk recording digital audio workstation. It works well with tools like Yoshimi and qjackctl, making it an ideal workstation. It also happens to be free on Linux and is about $45 dollars for the Windows and Mac bulids.
QjackCtl is a simple Qt application to control the 
JACK Audio Connection Kit sound server daemon for the Linux Audio Desktop infrastructure.
Yoshimi is a software synthesizer for Linux based on the 2.4.0 release of ZynAddSubFX, written by Nasca Octavian Paul. Yoshimi delivers the same synth capabilities, along with very good Jack and Alsa midi/audio functionality.
Reaper is a commercial offering similar to Ardour and is a fully featured DAW with additional plugins available. The standard license is $60 dollars after a limited trial period for the standard license and a commercial license of $225 for those whose revenue exceeds $20000
Reason is a highly sophisticated music and sound editing tool that comes with a big pricetag - $399. But you get what you pay for with this powerhouse. The music of Stardew Valley was made with this tool.
Scrienver is useful for folks writing up a complicated game, like an RPG or other heavy story influenced game. It's supposed to be a writer's tool, but works well for mapping out the plot points of a complex storyline. Also relatively inexpensive at $45 dollars.
Similar to above, except this software is more focused on making maps. Similar to a Computer Aided Design software, you can get the bundled offering for $99 with additional software options available for an additional fee.
Learning programming is necessary for building the truly great games out there. Many games use the simple Lua scripting language, but c# is a must for people willing to use heavy engines like Unity or frameworks like Monogame (see below).
Visual Studio is the ideal Integrated Development Environment for those looking to code games without the aid of an engine. A personal copy is free while commercial licenses for business are pretty steeply priced.
The XNA framework for creating games like Super Meat Boy, Stardew Valley, Fez, and Bastion used the XNA framework that forms the basis for MonoGame. MonoGame also happens to be 100% free and open source.
Comments
Very cool list, glad I stumbled upon this! Found it especially interesting you went one step further by adding "Music / Sound Workstations". Valuable list!