Do you want a built-in GPU (graphics processor), or would you prefer to use a 3rd party one, such as nVidia/AMD)?
What about the form factor (small vs. large - ie, desktop vs server-sized)?
(Not mobo or CPU related) What about power supply? This can be critical.
Manageability? Temperature sensors? ECC-RAM support?
All of these need to be taken into account. Example ECC-RAM will allow you to continue computing even if one RAM stick fails (this has saved my bacon on more than one occasion). Temperature sensor support allows you to monitor the thermal state of the system, and be proactive when stuff starts to overheat (see my comment on ECC-RAM).
As for the power supply, high-end video cards take a LOT of power, and not having an adequate supply has caused the melt-down of many motherboards and chip sets.