My wife commutes to school with her 15" macbook pro. she started off with a backpack, but it was too sweaty, and heavy on her shoulders. so she got a rack and a pannier. she likes it much better. it's still pretty heavy on that one side, but it's better than on her back she says.

she puts the laptop in a neoprene cushioned sleeve before it goes into the pannier, so it has the extra protection and is not just bouncing around.