The Philippines is not exactly the worst place on Earth as some of its places are business-friendly and tourist friendly. First, I would like to suggest places to go to for quality Filipino food would be in places like Cebu, Bacolod, Bohol and Iloilo. One may want to stay away from prolonged stays in places like Imperial Manila (especially Tondo). Imperial Manila is one place that's definitely going to make a tourist's longer stay a real nightmare most of the time!
I will talk about what to avoid first. In general, avoid those foods located at sidewalk eateries, foods prepared at the street, sidewalk barbeque or any place where it's located in a dirty area. One may notice the POOR SANITATION and POOR HANDLING should be enough to disgust anybody.. The problems with these places is their mediocre to really poor services and standards. Some of them may taste good but may require real stomach pills than your average bad cooking in a clean environment. And please, don't even try pagpag, food in the garbage is always food in the garbage!
Next, I could suggest a few places. Some of the best Filipino food restaurants in Cebu are Golden Cowrie, Tsiboom's, AA Barbeque and Conching's to name a few. Bohol has its famous Bohol Bee Farm which prepares some delicious meals. Surigao City well, you could actually taste some delicious delicacies at some of its commercial places, the Tavern Hotel's buffet serves some quality Filipino food. One may also consider that the food trip should be limited to commercial food establishments to avoid any "I won't eat Filipino food anymore" incidents. Some establishments may not offer all that great food but at least, one can prevent the food yuck incidents. Also be wary of commercial establishments that claim to be the best in town by their own ads and not by testimonials.
Note: It would be really best for tourists to write down their reviews of these places and recommend only Filipino restaurants NOT Failipino restaurants!