I didn't want to fuss around with rain covers. I would sometimes forget it at home or in the office. So when I started looking around for new commuting panniers my #1 requirement was that the panniers are waterproof. After some reading I bough Axiom Monsoon panniers and I'm very happy. I rode few times in rain, once in a heavy downpour and not a single drop of water inside my panniers.
http://www.axiomgear.com/products/ge...rs/monsoon-lt/
It's one big compartment, and the exterior is stiff, which some people dislike, but that's a trade-off for total waterproof construction. They also have a simple but effective locking mechanism that prevents them from jumping off of the rack when I hit a big bump.
Adam