Not only that, but some nano ITX boards have flat RAM slots and a sideways PCI express too.
Flat micro ATX cases are limited to the height of half-height PCI cards.
& @MechG:
I thought about the horizontal desktop rout, I built one for my parents. The problem with those is that they only tend to have a max of 3-4 3.5" bays, and this is also acting as a NAS. As you can see in the photos, this can hold 8 3.5" drives and 2 more 2.5" drives.
There is no way you could get a mATX board in there with a power supply, that's why I took the photo with the cd, that whole case is ~4 CDs of area on that side, it's really small. Max CPU cooler height is under 6CM for instance.