Isometric Pixel Art/Shading the Box
Isometric boxes, even if they're made of straight lines, can be made prettier through the use of shading.
Here we will learn about light sources and why the heck they're so important. If you leave off light sources, the whole picture will be off. So without further ado...
First draw a cube and pick your colors, each getting gradually lighter. There should be at least three, but you can toss in a fourth one if you want to do the last step (entirely optional). Shadows are usually less saturated than the other colours, but here i have kept the saturation high for stylistic purposes. Now pick your light source. I chose the upper right corner and drew a sun there to remind me where it is.
Flood-fill the spot that's facing away from the light source the most, in this case, the side I've labeled "1". Side "2" should have your next darkest color, and then side "3" should be lightest.
Swapping the light source should also swap your colors on the box. I put the sun in the left corner and mirrored the box to make it face the light source.
If you want to make it look a little different, take color number four and draw on all the black bits that ARE NOT touching the edge. The edges should remain black.
Hey, you did it!
Of course you can experiment with different positions for the light source. Remember to practice with the "sun" in different places so you get the hang of shifting the colors.