As the biggest flight guru here and after many hours in all classes on just about every airline, my recommendation is:
If flying coach, go American Airlines to HKG, then Cathay Pacific down to manilla. (and join AA platinum challenge before you leave!)
If you're doing it in business class - go Cathay Pacific the entire way. = FLAT++
If you are flying FIRST you need your head checked.
Go with oneworld airlines where you can, their inflight entertainment, seating and overall flight experience shits all over other carriers such as JAL, PhillipineAirlines etc that go that way.
Otherwise, if time is no issue, I'd probably pickup a Signapore airlines flight and go via SIN
Soo many options!!
Enjoy the trip!