It depends on if you will upgrade? If you system is going to be budget oreinted and will stay that way it doesn't make sense to put a top of the line mobo in it and surround it with budget components. On the other hand if you are going to upgrade it as money becomes available then start out with a better motherboard.
If you want to overclock or not should also come into the equation. Most reputable boards will work very well at stock speeds, but the more expensive boards offer more stability and overclocking options. If your not overclocking just find a board that has the features that you want because there will be little real performance difference between any boards on a given platform.
To sum up. If you want to overclock and or upgrade, get a more expensive board.
If not overclocking get a basic board with the features that you want and spend the extra money on CPU and GPU