Indie game storeFree gamesFun gamesHorror games
Game developmentAssetsComics
SalesBundles

just from playing their games, the 3D games like this one start with the Unity splash screen and the 2D games start with the Gamemaker splash screen. So Unity and Gamemaker Studio.  As for 3D art and animation I don't know what tools they use, but I can recommend Blender https://www.blender.org/.

Thanks! :)