Ortlieb's Bike Box series rocks.

Bike Box I
~$80


Bike Box II
$100


And the soon to come Bike Box III

I have the #1 & #2 versions and both are waterproof. The hardshell version can be locked.
All three connect to the rack with a quick-release plate.

I can fit my helmet, lock, and lunch in the #2 version, which is smaller than the #1.