Pretty much. There are standards for the motherboard and internal case form factors to prevent such problems. The most common form factor for a motherboard is the ATX form factor, and the most common form factor for a case is the ATX form factor. So if you get an ATX board and an ATX case, it will fit.
I believe that Intel recently tried to push a new BTX form factor (BTX boards and cases) that offered better cooling for their exteremely hot Netburst-based CPUs, but I suspect that those cases and mainboards will be fairly hard to find.
For the most part it's ATX, though there are some mini- and micro-ATX form factor boards out there, I believe that they will still fit in an ATX case.