The 3D effect is just from sprite stacks, where you draw sprites from bottom to top with Y offsets of -1 (or in my case -0.5, because it looked cooler). Additionally, you can adjust the lighting of each layer as you go, which will give a good 3D effect (I only used it for the player, really -- you can hit 'n' in-game to toggle it for everything to use). I used https://github.com/DarkDes/AsepriteSpriteStackEd with Aseprite to help with this, though I had to modify it to allow floating point layer offsets.