What should I do when my bags have been planted with bullets (or any malicious content)?

It's called Ninoy Aquino International Airport because that's it's name, it was renamed on August 17, 1987 with

the intention of honouring Benigno "Ninoy" Aquino, Jr., who was assassinated at the airport after returning to the Philippines from his self-imposed exile in the United States on August 21, 1983.

(From Wikipedia)

To your actual question, first there have only been a few cases of this reported (I've heard figures of 10 to 20 cases). Even if ten times more people just paid the bribe/fine and moved on that's still a fraction of a percent of the number of people that go through NAIA yearly. So, don't worry too much about it. It's undoubtedly a small number of people doing this out of hundreds that work at the airport.

Second, this has had massive coverage locally and internationally, it's unlikely they're still pulling this scam.

I'm going to paraphrase the advice my companies HR/Travel service gave which I think is good (if slightly over the top).

If a bullet is found, stay calm, deny any prior knowledge. Take a photo of the x-ray image showing the bullet and seek legal counsel. If you don't have a lawyer there's a public attorneys office. Don't open your bag without a lawyer, witnesses and airport police present and never touch the bullet.

If your fingerprints (which should, again, be taken only in front of your lawyer and police officials) are not on the bullet you will not be charged and you will get compensation.

Here's an article on Asian Journal that says the same thing.

Actually, the point here is to make it clear to the scammers that you're not falling for it. Once you start taking pictures and calling lawyers they'll probably just let you move on in order to avoid the problems you'll bring. But be prepared to follow through if they want to argue it out.

How can you avoid this in the first place -- just don't make it easy. Have bags without easily accessible pockets (or tie them all closed -- zip ties are good if you have a way to cut them open later, but locks or tape or even thread will put people off). Don't let your luggage out of your sight, particularly around helpful cab drivers and luggage porters who may be working with the scammers. Similarly watch loose pockets on clothes, etc.

In general, as with many of these things, they'll be looking for the easy targets. There are tons of people who go through the airport -- if it's obvious you've taken some precautions they'll know you know about the scam and move on to someone else (probably).

I've flown through NAIA many times and it's rare for people to actually touch your bags -- unless it's a cab driver or a luggage porter (which is why I suspect they may be part of the scam). So be watchful for people attempting to get close to your bags.

Edit: The same is true for any 'malicious content', stay calm, deny, document, don't touch and lawyer up. However judge your reaction on what is 'found', if something is seriously illegal or dangerous there will be people there who are not in on the scam and may react as if you're a real criminal. Staying calm is key.