Hi there,
Yes, Malaria is a problem, but lets not use scare-tactics here to freak out potential travellers.

The risk of Malaria in the Philippines is determined by the areas you are visiting. Check with your doctor, and let them know the specific areas you will be travelling to. I travelled to Manila, Alaminos in Pangasinan and Batangas, all on Luzon, and had no problems. My doctor said I could take a course of Malaria tablets if I wanted to, but didn't feel there was a pressing need for me to take them. This was backed up by my wife, who is a nurse and is from Bulacan.

By all means, take the course of tablets if you want to. Bear in mind, that no Doctor will tell you that the tablets are 100% effective, they interrupt your sleep terribly, and you need to take them for a number of weeks before travel, during travel and after you get back. This info comes from my brothers, friends, myself and my doctor, all of whom have travelled to southeast Asia.

Get a GOOD insect repellent. Not one from your local pharmacy or drugstore. Go to a reputable, well-established outdoor store, and ask them for the best insect repellent they have. Estimate how much you will need based on how much skin you will be exposing for the length of time you will be there. Then buy an extra bottle, just in case. It will cost you a few extra quid, but it will be worth it in the long run. Then make sure you apply it!

Always make sure you have travel insurance that covers medical expenses, and familiarise yourself with the procedure involved in case you need treatment.

You can't cover all eventualities when travelling. Trying to do so will result in you spending more time worrying than experiencing on your holiday. Do your research beforehand on the essential do's and dont's, apply these, and then just enjoy!