COMPLETED
UPDATE: (September 23, 2007, 8:10 GMT+8) Found a better source, namely the Wikipedia list of cities in the Philippines. It's source for population figures, in turn, is the Philippine government's census website for the year 2000.
SOURCES: List of cities in the Philippines,
Google Maps,
Tageo.com
NOTES: Makati is widely regarded as the nation's economic capital, Quezon City is a former capital, and the list follows the Wikipedia list, there are a few kilometers of discrepancies between sources, some cities (Batac, El Salvador, Palayan, Tagaytay, Tandag, Tangub, Trece Martires, Vigan) have less than 50,000 pop and may be removed (all I can defend is Tagaytay, which is really a popular local tourist destination)
_____
THE PHILIPPINES
14.651111,120.971716,Caloocan City
14.483333,120.983333,Las Piñas
14.550000,121.033333,Makati
14.668,120.948,Malabon
14.616667,121.033333,Mandaluyong
14.55151,121.034685,Manila
14.640000,121.097222,Marikina
14.383333,121.050000,Muntinlupa
14.667,120.950,Navotas
14.509,120.993,Parañaque
14.550000,121.000000,Pasay
14.560,121.079,Pasig
14.644,121.037,Quezon
14.633333,121.033333,San Juan
14.527,121.075,Taguig
14.700,120.967,Valenzuela
8.947501,125.545303,Butuan
9.124400,125.539900,Cabadbaran
8.855278,125.775556,Bayugan
13.133333,123.733333,Legazpi
13.237700, 123.540800,Ligao
13.359,123.734,Tabaco
6.706,121.971,Isabela
6.6568,122.1439,Lamitan
14.6751,120.5387,Balanga
13.76151,121.060501,Batangas City
13.94372,121.166801,Lipa
14.0846,121.1474,Tanauan
16.416,120.593,Baguio
9.648423,123.862602,Tagbilaran
8.1602,125.132,Malaybalay
7.910,125.099,Valencia
14.8429,120.8112,Malolos
14.755,120.9442,Meycauayan
14.814,121.045,San Jose del Monte
17.6186,121.7247,Taguegarao
13.41995,123.406403,Iriga
13.62589,123.178596,Naga
11.585,122.751,Roxas
14.48035,120.8936,Cavite City
14.103,120.933,Tagaytay
14.279,120.869,Trece Martires
11.0365,124.022,Bogo
10.1037,123.6458,Carcar
10.30723,123.898399,Cebu
10.52716,124.030296,Danao
10.30596,124.0131,Lapu-Lapu
10.324,123.922,Mandaue
10.211,123.758,Naga
10.245,123.849,Talisay
10.383333,123.650000,Toledo
7.0212,125.092,Kidapawan
7.3167,125.6847,Panabo
7.0858,125.709,Samal
7.3867,125.7957,Tagum
7.08008,125.613701,Davao
6.755000,125.355500,Digos
6.96,126.205,Mati
11.6114,125.4321,Borongan
18.0572,120.5546,Batac
18.19762,120.591698,Laoag
17.1868,120.4447,Candon
17.57,120.3759,Vigan
10.69688,122.570602,Iloilo
11.1042,122.6435,Passi
16.9318,121.7655,Cauayan
16.6875,121.5437,Santiago
17.4134,121.4441,Tabuk
16.6047,120.3156,San Fernando
14.2079,121.154,Calamba
14.07105,121.3265,San Pablo
14.303,121.1102,Santa Rosa
8.2328,124.240097,Iligan
8.002695,124.291901,Marawi
10.6731,124.8137,Baybay
11.00698,124.612801,Ormoc
11.24775,125.003502,Tacloban
7.223017,124.242897,Cotabato City
12.3561,123.6285,Masbate
8.485413,123.808998,Oroquieta
8.145755,123.841721,Ozamiz
8.064722,123.750198,Tangub
8.064722,123.750198,Cagayan de Oro
8.557124,124.524002,El Salvador
8.823268,125.102402,Gingoog
10.674907,122.951934,Bacolod
10.533333,122.833333,Bago
10.95603,123.308098,Cadiz
10.833,123.5546,Escalante
10.1084,122.8729,Himamaylan
9.9936,122.8154,Kabankalan
10.4249,122.922302,La Carlota
10.9348,123.4221,Sagay
10.4792,123.4145,San Carlos
10.80328,122.973999,Silay
9.7557,122.4132,Sipalay
10.7467,122.9706,Talisay
10.9035,123.0747,Victorias
9.595244,123.122299,Bais
9.3632,122.814,Bayawan
10.386,123.196,Canlaon
9.3007,123.3122,Dumaguete
10.12354,123.269699,Guihulngan
9.5123,123.1625,Tanjay
15.48902,120.968597,Cabanatuan
15.3086,120.9432,Gapan
15.7078,120.9044,Muñoz
15.533333,121.083333,Palayan
15.79006,120.987396,San Jose
13.404,121.1757,Calapan
9.7329,118.7701,Puerto Princesa
15.1442,120.591599,Angeles
15.0295,120.6891,San Fernando
16.1569,119.9797,Alaminos
16.0382,120.337196,Dagupan
15.928056,120.348889,San Carlos
13.9114,121.6272,Lucena
14.0285,121.5915,Tayabas
14.5763,121.1749,Antipolo
12.06994,124.600304,Calbayog
11.75961,124.889702,Catbalgan
12.9771,124.0106,Sorsogon City
6.116667,125.166667,General Santos
6.501398,124.846199,Koronadal
10.1312,124.8587,Maasin
6.692109,124.6772,Tacurong
9.784664,125.484398,Surigao City
8.1992,126.3164,Bislig
9.076904,126.199699,Tandag
15.4822,120.5939,Tarlac
14.83084,120.282799,Olongapo
8.657005,123.432198,Dapitan
8.6111,123.3482,Dipolog
7.829801,123.437103,Pagadian
6.90553,122.068604,Zamboanga City