The photos and videos on the new iPhone should have been imported by your computer as with any other digital camera before transferring the backup for your old iPhone to your new iPhone.
The first time you connect a new iPhone to iTunes that is used to sync with another iPhone or iOS device, you are prompted to transfer the backup for the old iPhone or iOS device, or set up the new iPhone as a new iPhone. This is designed to be done right away with a new iPhone.
Photos/videos in the Camera Roll are included with the iPhone's backup and when choosing to transfer the backup for the 3GS to the new 4S, the photos/videos that were in the Camera Roll on the 4S were replaced with the Camera Roll on the 3GS.
The photos/videos that were in the Camera Roll on the 4S are gone.