First, thing is first. No pannier recommendations. I mean it. It doesn't work for my commute and I spend about equal time hoofing it as riding throughout the day.
The requirements are:
Large - 45 - 55 liters or 3,000 - 3500 cubic inches
Waterproof - (at least have a raincover option)
Some kind of organization
Can handle about 25 - 30 lbs
Right now I have this -

It works decent enough. It is definitely waterproof but is nothing more than a garbage bag with some straps glued on. The straps/load carrying leave a lot to be desired.
I am considering:
http://www.rei.com/search?query=vaga...x=0&button.y=0
Pros - It is big, has a raincover, has some pockets, has an internal framesheet giving it structure.
Cons - Not actually waterproof only because of raincover. A bit on the small side. My pile of junk barely fits in here.

Pros - Waterproof, should be comfortable enough, I was happy with my messenger bag
Cons - A big improvement but still a garbage bag with straps.