I have recently learned in my graphic design class how to create orthogonal cubes using the line tool. We had three assignments. 1) Follow the Deke's Techniques Tutorial on Lynda.com 2) Expand on the tutorial 3) Create a new design
Here the product of the first design.
One of the take aways here was that Cmd+Y keyboard shortcut. This allowed for me to see only the anchor points and paths of the cubes. I chose these 3 colors because I wanted the viewer to get a sense of a rubiks cube. Next image is from our own creation. Still using the techniques of the tutorial but making it our own. 
A big take away from this is the Cmd+D command. The duplicate command allows images and shapes to be duplicated exactly how it may be rotated. I wanted the viewer to get the sense of being in a beehive. The squares reminded me of a honeycomb. Next image is another tutorial. Here a big take away is the rotate tool. You can have the rotate tool and copy the shape you are rotating. Also you can duplicate the shape and have the same rotation and the same gradient throughout. 
This gradient tool created an optical illusion. With our squares we created guides to make the shapes.