I think the one major advantage of waterproof panniers would be floatability. I bring this up because some might be considering rather extreme touring such as off-road and the like, and fording rivers with your bags tied behind you and your bike above your head is a very real possibility in certain situation (monsoon season in S. Asia comes to mind). On the other hand, one could easily take their non-waterproofs and put them in a plastic bag to achieve the same.
Many non-waterproof bag makers still add a plasticized coating inside to make them "water-resistant" so while I am not disputing the advice of others, I question the breathe-ability of such bags in general.
I have never had much of a problem with either version. I have toured with water resistants on the front and Ortleib rollers on the back, and never had mildew problems. Admittedly, it was a pretty dry Summer tour...
I would go with Ortleibs or Arkels simply for durability, their water resistance not withstanding.