Not much call for it, but they are out there. I recall the HAF stackers from Cooler Master, not sure if they are still for sale anywhere.
Looks like Thermaltake had a line of stackables under the XCore name. I keep seeing references that the Core V1 and V21 might be stackable as well.
Have you considered a larger chassis that accepts two motherboards? Very expensive for most of them. Most offer an E-ATX + a Mini ITX though.