On my last short bike tour, just over a week, I used a Burley trailer to haul my gear. On most trips, I've used panniers.

The trailer handled admirably and I often would check to see if it was still behind me. The weight was there, but no handling issues. The trailer also meant I did not have to worry too much about balancing the load, which becomes more important when using panniers. The biggest drawback is in trying to load the trailer in a bike box. Using a trailer also requires carrying spare tubes for it, since the trailer does not accommodate the same size tires as a bike. Oh, and it's also easy to pack way too much onto a trailer.

The panniers will affect the handling a little, but then everything's on the bike. It's also a lot easier transporting the bike without a trailer instead of a bike and a trailer.

I'm interested in which option you prefer and why.