I have a 2-wheeled Quik-Pak trailer, a Bob 1 -wheeled trailer, and racks w/panniers. I really don't like the Bob, just a pain to stop and park the bike for picture taking and what-not. The Bob just feels like its pulling the bike over to the side. I really like the 2-wheeled trailer, tracks nice, no side pulling on the bike, and I just don't really notice it back there. Its weight (13#) is about the same as front & back racks w/panniers. The only issue with the Quik-Pak is that I tend to bring too much stuff, since I have lots of room. Works great (for the kids) when I tour with them since I carry all the gear. I now only use panniers when I tour solo, since I've got my gear down to about 20-25lbs, so my needs for storage is much less.

As has been said, you've got to move whatever you bring, whether its on the bike or behind it. I don't believe there's any real measurable difference in resistance between using a trailer or panniers that a rider would feel.