I have been carrying my Fujitsu P-2110 subnotebook in the Medium Timbuk2 computer commuter messenger bag for about a year and a half without any problems. But my commute is really short and I don't work up much of a sweat.
When I've ridden longer in the summer, having the weight on your shoulder for a long time can result in a sore shoulder and a big sweat patch. Backpacks at least spread the load, but are even hotter.
You might want to check out the Ortlieb Office pannier. I would buy one if I had a longer commute (might buy one anyway). It mounts and dismounts quickly from the rack (I have Ortlieb panniers with the QL2 system and they are great). And it provides a lot of padding and some suspension. you can put some extra material (spare tshirt) in the bottom of the bag to offer additional shock absorption.
A more classic, but perhaps less convenient, option would be the Carradice office pannier. I say less convenient, because the mounting/dismounting looks a little trickier, but Carradice makes beautiful waxed canvas bags.
Either way I think your laptop will be safe on a pannier unless you are doing big drops off high curbs and as long as you avoid monster potholes. Laptops and hard drives are more rugged than you think these days, but if you travel with one at all...it's best to have damage insurance. A cracked display will cost you as much as the laptop is worth to fix it.
Many homeowners and renters policies have laptop insurance available, and some companies provided inexpensive laptop coverage as a stand-alone service. Oh... and backup your data regularly whether you carry the laptop on your bike or not.
Sean
