I use pet carriers : the ones with top and front doors are best. I have one size that takes a pekin sitting down and a larger size that takes a muscovy drake sitting down. Most dogcrates are too large for transporting ducks as the duck can stand up and move around, which is not safe. I have used a medium dog crate with front and side doors, with a divider, for 2 muscovy drakes. They sit sideways and although they have the headroom to stand up they are too confined in space to move around. When I had a tightly bonded pair of pekin drakes I could transport them in one medium dogcrate without a divider. I have also used a large heavy duty cardboard box: it had originally held a printer. It was a good size and with holes drilled round for air proved a good emergency carrier.
When I can plan a trip rather than going and picking a duck up in an emergency, I restrict their access to food ( but not water) for a couple of hours before travel. I offer them Pedialyte or Liquid IV solution every hour while traveling. They always sit on a puppy pad in their carrier, crate or box. Two of my current flock have traveled long distance with me several times with no ill effects.
I've put singles in softsided cat carriers. Not something you want for a long trip since they can't stand up but it's good for a 30min drive. Top and side access is handy and they are dark.
For groups I use a wire dog crate. Poop gets everywhere and they will slide around even with shelf liner or towels for added traction.