Yep, alphabetical order. I was using the NES controller just as a size reference thing. Maybe I should have done something with that extra space there.
You'll probably notice that Miracle Piano Teaching System takes up three spaces, that's so that the 678 games take up as much room as 680 would, which is a much rounder number to work with. 34 across and 20 down.
Now that I've had tons of OCD fun putting this together, I could consider doing something similar with other platforms. The Super NES has a great library too, unfortunately the right and bottom sides being black on most boxes would make it seem rather dark and any inconstencies in the scans would be even more noticeable.