^yes, the southbridge is sometimes too close to the GPU's PCB in case of mATX. Also, the heatsinks on the NB & SB are smaller incase of mATX, again leading to heating issues when OCing the RAM/CPU.
Moreover, using PCI cards (TV tuner or Sound card or expansion cards) isnt always a choice when using mATX because it spoils the air intake of the GPU's dual-slot cooler.
And in some cases where an aftermarket GPU cooler is involved (like in my case Accelero s1 rev2), the GPU may use a whopping 3 slots! The mATX just cant cope up with the space shortage here. Hence always stick to ATX (until its out of your budget).