Some of my faves after spending several weeks throughout the country:

Boracay: Very beautiful island with an amazing white sand beach and crystal clear water. I spent an entire week scuba diving without doing the same dive twice and would go again in a second. Mostly Filipino vacationers except around the holidays. Good nightlife if you like relaxing on the beach listening to live music. While I don't have specific information about luxury hotels, they are there and you can spend upwards of $400-$500/night.

Pearl Farm: Off the coast of Davao on Samal Island. Nice resort with very clear water and lots of marine life. Somewhat boring in that the only easily accessible nightlife is the outdoor hotel bar but would still make for a few nice days as part of a longer venture to Davao / Mindinao.

Bohol: If you're going to or through Cebu, add a day tour to Bohol. There's a standard tour which includes a boat trip on a beautiful green river, the chocolate hills, tarsiers and a visit to one of the beach resorts. If you have the time, you may want to spend the night at one of the resorts - some looked decent but I didn't see anything luxurious.

Manila: Not so much a fave but you're likely going to pass through anyway. Stay in a nice hotel in Makati or Ortigas, visit the bay front promenade to see a sunset, shop at any one of the many very large shopping malls, and take in some history - Intramuros being pretty cool.

Baguio: Haven't been but this cool mountainous resort town is next on my list of places to visit.