originally they were done in photoshop as 2d art. I was going to use the same system here, but went totally 3d. I took the 2d elements I previously did and added them to my 3d asset sheet. All the graphics are a single 64x64pixel sprites packed into 16x16 (256 in all). I use some custom shaders to decide which is the starting graphic and the size and width.
I also used a custom written sprite editor to draw some of the the other textures. There is a custom 3d app that takes everything and also allows me to create lowpoly models and texture map them very fast.
The shaders also allow me to use different colours when rendering so most of the graphics are in grey. Using this way means I can use the same graphics in different colours giving totally unique looks without loads more work