Sorry to come in at the end of an old topic like this, but I have having almost the same problem as the original description. The difference is that I have a Quad running Tiger and the Apple Shipped HL-DT-ST DVD-RW GWA-4165B is making the same annoying periodic noise as it tries to spin up an empty disc tray.
I recently purchased a new main SATA drive and installed the OS from scratch, so it's very possible that I have my Energy Saver settings much different than I ever had before. Previously, I had been running for about three years with updates only, never a clean install, so my settings had been preserved. This time, I did not clone my drive or take advantage of the feature to move my account over from the old drive. One important different is that I used to have Energy Saver set to never sleep, thinking that this was necessary for Logic Studio Pro to operate fully. However, now I want to save on my electric bill, and I have things sleep after 10 minutes, including the hard drive.
Is there a known issue with Energy Saver settings which might cause repeated access to an empty DVD, even when the hardware is Apple original? (except the new SATA disk drives)