It depends on the case if your not using a small case that a ATX board will not fit in then a mATX board, if your using a bigger case that a ATX will fit in with a side window then the mATX is going to be tinny and looks funny to me.
If you wish to run SLI or Xfire than a ATX board with 3 slot spacing on the PCI-E X16 slots or if your like me (I have 6 drives in my PC) then again a mATX case just don't cut it.
What to get really depends on the looks you like how many drives you need and the rest of the parts. A small cheap mATX case might not have adequate cooling for the parts.