HTPC is just a name that refers to usage, not size.
You can buy a shelf type "HTPC" box that is full ATX, or micro ATX. Similarly, you can buy a "tower" case that is micro ATX.
So, you have to ask yourself what you want aesthetically. Smaller cases will typically have poorer airflow, and will be more difficult to assemble, but blend in with stereo and home theater components.