Awesome thread.....
Couple of things I do I picked up some waterproof camping bags at walmart a set of three smaller ones and one large one that would hold a sleeping bag. I use them for my clothes even though my panniers are water resistant. I just dont trust the shopping bags. My commute is much shorter though... only 4.5 miles one way. I have ridden in a tropical storm however with my clothes in one of those bags and never had an issue.