Yes in these case:
- mobo with different chipsets (north-bridge)
- mobo with completely differently different specification, like ddr2/ddr3 support
- quality of components
- board layout, design, components placement (may not directly with performance, but it affects cooling, cable management, and hampers OC)
- mobos from different manufacturer, mainly because of different components, layout etc.
No in this case:
- Exactly same mobo from same manufacture with same base chipsets and specs.