It's all the same as a full sized ATX motherboard. The only thing different is the size. The Mini-ITX boards use less power too, but as far as building them and parts, it's all the same (with the exception that some of the VIA ITX boards have the processors built in instead of adding one on).
If you need something that doesn't use much power, and can be squeezed into tight places, go mini-ITX. If you need something with lots of power to do stuff, and is in most cases a bit cheaper, go full sized.
I personally prefer micro ATX, same thing as ATX just smaller.