Form-Factor
Motherboards have different form factors -- the size, shape and design of the actual motherboard. Nowdays, for a PC the most used form-factors are mATX(microATX) and ATX. For more information about form factor you may check this link : PcGuide.
Additional Integrated Motherboard Functions
On some motherboards, circuitry is included to perform some of the common functions normally found on expansion cards. This definitely has its pros and cons, depending on what is included, how they do it, and what your needs are. In general, incorporating built-in circuitry has the advantage of lower cost, and the disadvantage of lower choice and upgradability. In addition, the cost savings of integrated components only translates to real money if you use them! If you end up adding a SoundBlaster and your own video card because you don't like the integrated components, you aren't saving any money at all. And you can't sell the integrated devices to someone else, obviously.