In the past few years quite a few major Airlines have suspended or reduced their flights to the Philippines due to lacking passengers or other economic reasons. However, in the same time domestic carrier Cebu Pacific has updated it's fleet from old DC9 to modern Airbus aircraft and beside domestic destinations, is now also serving neighboring countries like Hongkong, China, Taiwan, Singapore, Malaysia and Thailand as a budget carrier.
Other budget carriers from the region, like Tiger Airways from Singapore or Air Asia from Malaysia have daily flights to and from Clark Airbase in Angeles, Pampanga, north of Manila. This makes it possible to make a quick Visa Run or holiday to any neighboring country for just a few Dollars. Air Asia now also offers domestic flights in the Philippines.
Air Asia also offers some long distance flights to and from some destinations in Europe (Paris and London) and Australia. The prices are very reasonable but you always need a connection flight to the Philippines, which adds up to the costs.
Another way to get cheap flights to the Philippines is a Balik Bayan or Ethnic Ticket. These tickets are usually offered by some specialized Travel Agencies in your country. For Germany this is Vollmer Reisen in Rottenburg or Kirschner Reisen in Cologne. To buy an Ethnic Ticket, you must be either a Filipino or being married to a Filipino citizen. Ethnic tickets are usually about 100,- € cheaper than a regular ticket and offer other candies like up to 35 kg free luggage or a validity of 6 or 12 month.
The cheapest flights from Europe into Manila or Cebu are currently offered by the airlines from the Middle East like Qatar Airways, Gulf Air, Kuwait Airways, Saudi Arabian and Etihad. If you are from the US, look out for flights with Cathay Pacific via Hongkong or Asiana Airlines via Seoul in Korea.
Most Airlines have Manila as their destination Airport in the Philippines but some also offer flights directly to Cebu, like Asiana, Cathay Pacific, Korean Airlines, Qatar and Singapore Airlines (from Singapore to Cebu by Silk Air). Flying to Cebu directly could save you the connection flight from Manila if your final destination is somewhere in the South of the Philippines (Visayas).
New from March 2016: Emirates will start flying directly from Dubai to Cebu and back via Angeles (Clark)