It's the normal slop in the drivetrain. Most everyone with a GTO has experienced this. It's more prominent in the maunal cars. Basically it will pop or clunk when the driveline goes from unloaded to loaded (at a stop and go to take off) or loaded to unloaded (driving and you let off the gas or push the clutch in).
The rear ends on the GTO's were setup with terrible factory specs. Factory backlash is .007" - .012". It should be down around .005. So basically there's a gap between the ring gear and pinion gear. When your moving the gears are meshed and everything is ok. When the driveline is loaded or unloaded the ring gear will clunk against the pinion gear because of that backlash gap.
Here's what I did to get it to go away 90% of the time:
Rear Subframe bushings
Rear Diff insert bushing
Poly motor mounts (Hinson)
Trans Mount with Revshift Bushing Insert
That stuff took a lot of play out of the driveline and quieted down the clunking. It would still happen here and there but not as bad as stock.
Just recently I got a replacement Rearend under extended warranty (ruined my original at the track) and its waaaayyyy clunkier then my original rearend. So depending on how bad your diff is set up, you may get it to go away with the stuff mentioned above, or you may always have it... Unless you have your rearend rebuilt. I'm so tired of the clunking from this replacement rearend, I just bought a Truetrac Diff and am having my original rear rebuilt.
Hope this info helps!
2006 GTO M6
Motor - Stock with Vararam
Bunch of suspension
Bunch of brakes
12.81 @ 110.6 2.03 60'