I just finished a ~250 mi trip across Western Kansas into Eastern Colorado and used the BOB trailer instead of panniers for the first time. I thought I'd share the pros and cons I discovered. I was pretty heavily loaded, though I didn't bother to weigh it all, generally I just as soon not know, I just take what I think I might need and figure that's what I have to have. If I didn't use something I won't take it next time.
While riding I loved the trailer. I barely knew it was back there other then hearing the flag flap around. Keep in mind this was western Kansas and Eastern Colorado so the terrain was quite flat. The bike handled better then with panniers. I had some pretty strong cross winds and I think the low profile of the trailer helped not get pushed around so much by the wind. Also, there was clearly less weight on the rear wheel and it was the first trip that I didn't get a flat. Even though that may be because it was just 250 mi and also the road in Kansas was very clean, very little debris.
When it cane to walking the bike around or parking it though it was a different story. It was quite a pain trying to maneuver the bike as if you tilt it any little bit while walking it around or trying to park it the trailer would want to pull it over. I have a double kick stand and when I used it I had to be very careful that the trailer was lined up just right or it would tip over easily. In fact it did tip over 3 times, 2 of which could be attributed to a strong wind, but one was strictly due to not balancing things well. Also it was very difficult to get into the bag without the bike tipping over. I have decided that in the future I'll only take with me what can fit in the trailer bag, but I'll also have a rear rack that I'll put things that I might need to get to easily, like my camera or rain gear if the weather looks bad.
Since I spend a lot more time riding the bike then walking it around I have to say I preferred the trailer to panniers. So, when I do longer trips on easy terrain I'll probably use the trailer. But, for shorter trips, day trips or just single overnighters, I'll probably stick with panniers. I haven't tried the trailer in the mountains yet so how it impacts climbs I can't say. I may just not want the extra weight. We'll see.