>> I imagine having the boards vertical assists convection cooling,
>> assuming there's free (or forced) airflow from below, through the
>> cage, and out the top.
>
>There isn't; the airflow goes the other way.  There is a bank of fans
>(9? 12?) at the bottom of the cardcage that pulls air down over the
>cards and out the bottom.

   Are you sure you have the fan tray right-side-up? All of my chassis blow
out the top.

>> Are cooling problems common with 'wide pizza box' machines?
>
>In my experience, yes.  I think I've lost at least one CPU board to
>overheating, and come close to losing others.

   I've never tried running anything wider than a three-slot chassis on its
side, but those have done fine. With all three fans going, there's LOTS of
airflow. Channel it into a narrow duct and you could dry your hair.

   --James B.