Smaller is better for multiple reasons. If you are building a HTPC, then smaller means less real estate taken up on the shelves and stands around the screen. It also means less weight to transport when going to LAN parties.
Smaller is king for space under the tv and the challenge of building in a small form factor case. That and my eight year old, Core 2 Quad Shuttle is up for retirement and my wife would not be happy if I went out to buy parts for a new SFF HTPC.