There are a couple of ways of flying into the Philippines from Europe. The two most frequented International Airports are Manila and Cebu.
Almost every Airline is flying to Manila with only one stop, while Cebu is only serviced by a few like Cathay Pacific , Asiana and quite new, Emirates with a one-stopper. From Manila you can, of course, reach every destination within the country for small money with Philippine Airlines.
It is really worth to compare and sort out, whats important for you. Saving time or money? Also, I can recommend a Stop-over in any of the big Cities, where you have to change planes.
I really do not have a preferred Airlines. All of them, flying to Asia, have a good Service, good onboard Entertainment and enough space for a 1,90m guy in Economy.