Standard ATX mobo will fit all cases exept micro ones (then of course you would need a micro-ATX mobo).
As for advantages and disadvantages, it really depends on what 2 cases your comparing, there are many dffernt types and design, what 2 are you looking at?? Do you have any pictures of them. If your jsut building a standard home PC then a full tower or even something a bit smaller would do fine, really you only need a server case if you.... building a server. They usually have a lot of cooling oppurtunities and not very many drive bays, not really for a home user at all!!