Mostly just the size. But the size effects how many PCI/RAM slots it has. So with a micro atx motherboard you would not be able to run three videocards, maybe not even two.
ulfsark basically covered it but I wanted to add something.
if you look at an ATX mobo with some enthusiast features (not fully decked out, but not bottom of the barrel), and then look at a mATX with all those features, the mATX will be more expensive.
Big premium for feature-rich mATX boards, but similarly priced to ATX with less features.