Non Xfire/SLI boards are usually mATX board or low budget board. These boards are usually inferior performance-wise or feature-wise.
For example, these boards would be cutting corners and use cheaper components, so they would be harder to overclock.
These boards can also lack desired features like native RAID support, native Firewire support, extra SATA ports, CLRCMOS button, board layout that makes sense, ...etc.
You should base you board decision on the features you want, not the features you don't need.