I use a pannier to carry my laptop and other stuff (clothes, lunch, etc.) and I like that better than a backpack. I found the backpack made me too top-heavy and it made it too hard for me to look back left or right without losing my balance. Plus, I have some back trouble and its better for me to keep excess weight off my back (YMMV).
Most panniers do have some give/bounce which helps absorb potentially damaging bumps. After 3 months of travel like this (several hundred miles) I've had no problems yet, and this includes one accidental fall where the laptop-side of the bike hit the ground with no damage to the laptop. Again, YMMV, and I will say that my route is probably smoother than yours--no cobblestones for me, thankfully.
I put the laptop in a neoprene waterproof laptop sleeve which is a good protector from water and vibration and most bumps. The sleeve came with a thick foam insert (the size of a laptop) as packing material, and I use that as additional vibration absorbing material. I put the foam insert in the pannier bag on the bike-side. This is what I bought:
http://accessories.us.dell.com/sna/p...9&sku=330-1274
One thing I've read is that laptops with SSD are more resistant to the rigors of bike commuting than traditional hard drives, which have more fragile moving parts. So, if you don't have a SSD, get one. Not only will it be more durable, but your computing experience will be much faster! The only downside to SSD is they're more expensive and have less storage. Unless you have to store large amounts of data on your laptop, then this is not a problem for most people.
FYI, I use the Bontrager City double pannier and it fits a 15" laptop with protective sleeve just right.
http://bontrager.com/model/07726
If I pack everything carefully, and put my clothes in ziplock plastic bags, I've never had anything get wet.