Matching the Motherboard to the HTPC Case
Various HTPC case sizes are available; they might be reconditioned PC cases or specially designed HTPC cases, with front panel slots for displays and other additions. Once you have chosen your HTPC case then you should choose your motherboard to suit it.
Just as there are different HTPC case sizes available, there are various suitable motherboard form factors.
The most common motherboard form factor is ATX/Micro ATX, which are variations on the same design. For HTPC purposes you should be using a Micro ATX motherboard, identifiable by the square design and position of RAM on the right hand side of the CPU, while the PCI and PCI-e expansion slots will be found at the opposite end.
Conversely, and if you are building from scratch (as opposed to buying a case and making your HTPC from spare components) the BTX form factor (used in PCs such as the Dell GX6xx series) is a good alternative; while taking up a similar amount of space, the BTX form factor has a different arrangement of the components with the memory modules effectively “swapping places" with the PCI-e slots (most importantly the graphics card) in order to benefit from the same airflow and therefore require few fans.
As you probably don’t want your HTPC to be noisier than your PC, fewer fans is probably a good idea, so the BTX option might be attractive to you. Note that a BTX motherboard requires a BTX case - BTX and ATX are incompatible thanks to the arrangement of the expansion slots.