Whatever you do, make sure that Bluetooth is either off, or "Allow Bluetooth devices to wake this computer" is not enabled. There are stories of MacBooks turning themselves on during transit due to Bluetooth. Also be absolutely sure that it is in fact asleep when you put it in the bag; the light should be pulsating when you do so.
However, with everything said above, I personally do not transit my MacBook Pro while in S3 sleep mode. I only transport my computer either powered off, or in S4 sleep mode, which can be done using the "Deep Sleep" widget. In S4 sleep mode the computer is off, and the contents of memory have been written to the disk.