The noise could be from a couple of things that I'm aware of. (Perhaps it could be from another source but I'll leave that up to others to divulge ...)
It could be the duct, itself, 'popping' when air is either drawn into a return duct or when air is vented out the register. It's kinda like the 'state' that, say, a partially-crushed plastic bottle is in when you go to either suck out the air or blow air into it. Either way, the bottle will kinda 'pop'. Soooo, depending on which duct is popping, that will help determine which one is causing the popping. Of course, NOW what do you do?
Well, you could brace the duct or replace the 'damaged' section. HOWEVER, before you go too far, the popping could be a problematic-sound that's coming from the blower.
Here's what I'd do. SPend a couple of 100 $$$s and hire a Pro to do a COMPLETE inspection of your HVAC system. DO include the A/C; not just the heat side. If you've never had one done, or if it's been a number of years since you've had one done, it is $$$ well spent.