The main two difference is the power consumption and the size.
The desktop boards takes more space and eats a lot of power. There are bigger power supplies now that can handle them, but some people still prefer small and efficient boards.
That setup would work if you have a proper powersupply.
The alternative to desktop board is the mini itx boards that fits into the voompc, right now the intel dual core atom is very good and very inexpensive. That should be a good start for you