Depends on the laptop. My first one was a behemoth of a laptop, but after it tanked I bought something about half the weight and 2/3 of the size (but 3 times the machine, funny how that works). I just throw it in my backpack now. I don't like using my backpack and would rather use my panniers, but I wouldn't feel safe with it in the panniers, bouncing around. I know that the suspended cases are supposed to help, and supposedly they work, but I wouldn't trust them.

Oh, and make sure however you shut it down or suspend it that the hard drive has stopped spinning. I can't tell you how many machines I saw when I worked in support that had damaged hard drives that the user admitted to having transported with it still running. Now if you've got one of those fancy schmancy SSD drives its a different story but its still a good idea to shut it down to transport.