I visit Manila regularly and check out its beautiful churches all the time. The church of San Augustin always astound me, even if I visit it a lot of times. However, it usually is closed, but can be accessed via the monastery, which also doubles as a museum. For a sum of 100 pesos, I can visit the museum and also I am granted access to the choirloft. This gives a breathtaking view of the church. A must see! I really like the trampe'oleil paintings and the lectern on the choirloft. The exterior is very simple, actually not that impressive on my opinion but do check out the carved wooden doors on the portals and also the chinese guard dogs- a perfect example of east meets west influence.
Another notable church is the San Sebastian. It is a complete stand out, being built in Neo Gothic Style, not common in most churches in the Philippines. Also it is made entirely of steel! A rare gem. And the good part is, it is always open! Even if the portal doors are closed, just go to the small door on the right side of the church, walk past the small, office like room and to a sort of courtyard where the side portal of the church is kept open. It is usually empty. Perfect for quiet medittation and prayer.