The board that will be the "brain" of the bot will be it's motherboard weather you put one or more uC's there and some sensory circuits or if there is CPU + RAM + controllers and expansion slots ...
If we assume that term "motherboard" means "PC motherboard" then:
It really depends on what do you want your bot to do ... if you want your bot to follow the line, answer to simple stimulants ... for e.g. keep going straight on different surfaces, avoid obstacles etc .. then uC is more then enough .. on the other hand, if you need heavy calculation in order to perform very complex tasks autonomously then you need to go with more complex solution then simple uC ... depending on the complexity, you go from single to multiple uC's up to a motherboard ...
If you want PC based MB, *ITX boards are great, they have everything, do not use up too much power, run on DC, can boot from CF, no moving parts ... can handle lot of stress ..
the only "issue" is, you need to "hook the mb to your drivers" so your MB will control rest of the robot via usb/parallel/serial port .. (the gumstix is in many cases better for embedded solutions but bit harder to program)