You may try searching the Forum under trailers and bob or yak and you will find many posts in favour of the BOB. I am leaning towards the BOB trailer myself and I have toured with panniers in the past and invested a pile of money into them. Money wise, I think they are about the same amount if you are starting off fresh. The BOB bag is better for water resistance and can be used for other things like a canoe trip, for example and the trailer can be used for getting groceries easer then using panniers. I would think the trailer would be easier on the bike in the long run and fewer things to brake, get lost or stolen. Also, with a trailer your bike does not necessarily have to be as robust as touring bike. There are many other things to consider such as wind resistance, transport on trains, planes, etc.
Regards
Gordon p