Only done it once. I put my two panniers back to back to protect the mounting clips, then got one of those baggage wrapping places at the airport to wrap them together. They went as one piece of checked baggage and I had no problems.
thats what I've done in the past. My only other piece of advice is, if you carry spares, prepare to be searched! Staff at Schiphol freaked out when my bag went through x-ray (years ago before the tighter security). I had put spare batteries, tools, computers, in a plastic bag and then wrapped spare cables around them.
It did look scary on the x-ray (wires, batteries, circuit boards!!). They were actually surprisingly nice after getting over the shock.