I've toured with both - front and rear panniers, and a Bob trailer. I prefer the panniers. The trailer felt like it weighed me down far more. Handling wasn't an issue - I usually had to double check after a stop to make sure I hadn't left the trailer, because I couldn't feel it back there. However, climbing a pass was different - I could definitely feel it. (I started thinking of it as "the anchor".)

A Bob is a great option for touring on bikes which aren't set up properly for panniers. You can carry everything in the trailer. I think I'd also use it if I was touring on dirt roads or trails on my mountain bike. But for riding on roads with my touring bike, give me panniers.