Of all the genres that run as smooth as silk in the context of a Philippine setting, it would have to be Urban Fantasy or Horror. The Filipino culture in general is one where superstition rubs shoulders with faith, and just about anyone can tell you two to three different superstitions that they follow. Filipinos are well aware of the Chinese practice of Feng Shui, for example, while making certain to check the horoscope every morning, while making sure to hear Mass every Sunday.
This sort of open culture leads to a whole bunch of interesting scenarios. Filipinos tend to enjoy the fantastic, from ghost stories, to urban legends to tales of creatures like the tikbalang or the kapre. Majority of the supernatural types that are common to Philippine beliefs are mostly those of the Fae and Ghosts, but there’s always room for the creepy undefined stuff.
A World of Darkness game set in Manila would be a perfect fit. The large socio-economic divide between the rich and the poor is nothing new here, and many crimes and deaths just pass unnoticed by the general populace, already far too numb to care anymore. The Media is obsessed only with the next scandal, and businessmen and politicians tend to have other priorities than being of help the their fellow man.
Personally, if I were to run Urban Fantasy or Horror in Manila, I’d go for Changeling: the Lost. The idea of being taken away and changed, before finally making it back is one that works wonderfully well in a Philippine setting. There’s always talk of people being taken away by some form of fae creature or another, and every child is taught to never accept food or drink if one was ever taken away, or else they would never be able to leave.
Sadly, the Cthulhu Mythos is probably not quite so applicable here, unless you try and force it and correlate the siokoy myth with the Deep Ones. If one veers towards non-fantastic horror, then serial killers and the like would be interesting in a Philippine setting. We don’t really get reports of serial killers here, but that might just be because the people don’t recognize it as such.
Overall, an Urban Fantasy / Horror campaign set in the Philippines would be an interesting mix of Asian and Western sensibilities. The fact that a lot of places here are ripe for some truly horrifying scenes makes it an even more fertile ground for bone-chilling campaigns.