I vote for Panniers! I have a Bob Yak, and will still use it some . . . But I like panniers better also! In addition to the points that Baz made, I find managing the bike easier with panniers vs a trailer. I find managing my stuff easier also. The dry bag with the Bob is not exactly handy when retrieving items either. One cool use for the bob though, and I have posted this before, is that you can unhook it and flip it over, and it makes for a pretty cool cooking surface/eating table! Also consider that this is my opinion as someone who has toured on a single bike with one/two others or solo. I might suggest that you post this same question in the tandem group. I am sure there are experiences specific to tandems that I for one would never consider, as I have never owned one . . . .

Also, I think panniers look cooler too!