Below is a "Directory of Cultural Heritage Churches" in Metro Manila which used to be found in http://www.aam-rcam.org/vim/index.htm but is no longer online. I was still able to salvage it from the Google cache. I'm sure there are more since Paranaque has several others such as the Redemptorist Church in Baclaran and the San Dionisio Church for example; and schools have charming churches and chapels as well such as the Abbey of Our Lady of Montserrat in San Beda College and the Chapel of the Holy Sacrifice in UP Diliman which is both a National Historical Landmark and an Important Cultural Property. Visiting all the churches below is one adventure worth doing in the near future.
Archdiocese of Manila
1. Minor Basilica of Immaculate Conception (Manila Metropolitan Cathedral), Intramuros, Manila
2. Minor Basilica of San Lorenzo Ruiz (Binondo Church), Binondo, Manila
3. Minor Basilica of San Sebastian, Plaza Carmen, Quiapo, Manila
4. Minor Basilica of the Black Nazarene (Quiapo Church), Plaza Miranda, Quiapo, Manila
5. Monasterio de Santa Clara (demolished recently to build Katipunan flyover)
6. National Shrine of Our Lady of Lourdes, Kanlaon cor. Retiro Sts., Santa Mesa Heights, Q.C.
7. National Shrine of Saint Michael and the Archangels (San Miguel Church), J.P. Laurel St., San Miguel, Manila
8. Nuestra Senora de Gracia Parish, Bernardino St., Guadalupe Viejo, Makati City
9. Nuestra Senora de Guia Parish, M.H. Del Pilar St., cor A. Flores St., Ermita, Manila
10. Our Lady of Loreto Parish, Bustillo St., Sampaloc, Manila
11. Our Lady of Remedios Parish (Malate Church), M.H. Del Pilar St., Malate, Manila
12. Our Lady of the Abandoned Parish (Sta. Ana Church), Pedro Gil St., Sta. Ana, Manila
13. Sacred Heart of Jesus Parish, Old Santa Mesa, Sampaloc, Manila
14. Saint Anthony of Padua Parish, Singalong cor. San Andres Sts., Malate, Manila
15. Saint Anthony of Padua Shrine, Manrique St., Sampaloc, Manila
16. Saint John the Baptist Parish, Pinaglabanan St., San Juan, M.M.
17. Saint Joseph Parish, Juan Luna St., Gagalangin, Tondo, Manila
18. Saints Peter and Paul Parish, D.M. Rivera St., Poblacion, Makati City
19. San Felipe Neri Parish, Boni Ave. cor Aglipay, Mandaluyong City
20. San Fernando de Dilao Parish, Paz St., Paco, Manila
21. San Vicente de Paul Parish, San Marcelino St., Ermita, Manila
22. Santa Clara de Montefalco Parish, P. Burgos St., Pasay City
23. Santa Cruz Parish, Santa Cruz, Manila
24. Santo Nino Parish, Jesus St., Pandacan, Manila
25. Santo Nino Parish (Santo Nino de Tondo) I. Chacon, Tondo, Manila
26. Santuario de San Antonio, McKinley Rd., Forbes Park, 3117 Makati City
27. Santuario de Santo Cristo, F. Blumentritt St., San Juan, M.M.
28. Shrine of Our Lady of Correa (San Agustin Church), Real St., Intramuros, Manila
29. Archdiocesan Shrine of Our Lady of Guadalupe, 1923 Orense St., Guadalupe Nuevo, Makati City
Diocese of Cubao
30. National Shrine of Our Lady of the Holy Rosary (Santo Domingo Church), Quezon Ave., Q.C.
31. Santuario de San Pedro Bautista Archdiocesan Shrine, San Pedro Bautista St., SFDM, 1104 Q.C.
Diocese of Kalookan
32. Immaculate Conception, Gen. Luna St., Concepcion, Malabon, M.M.
33. San Bartolome Parish, Rizal Ave., Malabon, M.M.
34. San Jose de Navotas Parish, M. Naval St., San Jose, Navotas, M.M.
35. San Pancracio Parish, La Loma Cemetery Compound, Grace Park, Caloocan City
Diocese of Pasig
36. Immaculate Conception Parish, Plaza Rizal, Malinao, Pasig City
37. San Roque Parish, B. Morcilla St., Pateros, M.M.
38. Archdiocesan Shrine of Saint Anne, Santa Ana, Taguig City
Diocese of Paranaque
39. Our Lady of the Abandoned Archdiocesan Shrine, National Rd., Poblacion, Muntinlupa City
40. Saint Andrew Parish, Quirino Ave., La Huerta, Paranaque City
41. Saint Joseph Parish (Bamboo Organ Church), Diego Cera Ave., Las Pinas City
42. Santa Rita de Cascia Parish, Quirino Ave., Baclaran, Paranaque City
Diocese of Novaliches
43. Our Lady of Mercy Parish, Dumalay St., Quirino Highway, Novaliches, Q.C.