+1 on the Arkel Commuter pannier! I've been carrying my laptop in it most days for the past year, through the torrential Pacific Northwest winter, and I'm really happy with it. The material will probably take quite a bit of water before it wets through, but I've been using the accessory raincover. The suspended, somewhat padded laptop sleeve holds the computer very snugly, and Arkel's mounting system is rock solid on the rack and removes with one tug. It was expensive, but I'd buy it again.
http://www.arkel-od.com/panniers/com....asp?fl=1&site=
A lot of people swear by Ortlieb, and they have a laptop pannier as well:
http://www.rei.com/product/768571