Conformal Coating PC Parts?
There are coatings meant for this purpose (that is, coating circuit boards to improve robustness of the system with respect to corrosion and condensation etc.) I cannot imagine you running into a lot of issues with solvents using those products. Consult the datasheet to be sure.

PCBs used for computers have a lot of controlled impedance traces for different busses, like PCI(e), your DDRx RAM, high-speed busses to connect to the chipset, etc...

I don't know how controlled these impedance are, but coating them will effect this impedance.

In addition, coating everything will add thermal resistance to the system. This could mean that devices that were cooled through the PCB before with big copper planes no longer receive adequate cooling. This could result in components overheating and the board no longer functioning as it should. 

And of course (but I assume this is obvious) - you need to make sure that all the connectors and screw lugs are protected so they don't get coated. The locations where you screw the motherboard to the case are usually connected to some form of ground, and if this is not connected I think this could result in issues with EMC.

And I would be very surprised if there are no manufacturers out there that have conformally coated motherboards for industrial or other "high reliability" applications.