El Dorado Beach Resort, Dauin, Negros (2 towns south of Dumaguete) - A good place for divers, not a great place for beach goers.  No cottages on the beach, just the restaurant and the dive shop.  Brown sand beach, deep, always with a surf (at least in December).  Standard room $24, AC, cable, native style.  Food ok, pool, Swiss owned, with Sea Explorers dive shop and boat.
Coral Cay Beach Resort, near San Juan, Siquijor Island - Beautiful beach, white sand, large cottages, $26, native style, some on the beach, no TV or AC.  No dive shop, beach is shallow for a long way out, no surf.  Food pretty good, sw pool, American owned.  Dive arrangement is with Splash/Sea Explorers at Coco Grove resort (short ride away, free, can't pick you up by boat; too shallow).
Coco Grove Beach Resort, Tubod, Siquijor Island - similar to Coral Cay, maybe not as pretty.  Fresh water pool.  Sea Explorers dive shop next door.
Sibulan Dive Resort, Sibulan, Negros (1 town north of Dumaguete) - Small place, like a bed and breakfast for divers; the German owner does all the cooking.  Great food, expensive, tree house is $55 with AC and cable.  Great diving at Sumilan Island, Cebu - best visibility of the trip and near-pristine corals but no big fish.
Bethel Guest House, Dumaguete City - Nice place, on the bay, big rooms, AC and cable, P1600 for the family rooms facing the water.  No smoking or alcohol!  Food bad; go to 'Why Not' restaurant 2 blocks up.
St. Maria Hotel, Dumaguete City - Not bad, across from the market at the park, 2 blocks off the bay.  Very reasonable, P800 to P1200 for rooms with AC and cable.
Aloha Hotel, Roxas Blvd., Malate Manila - Kind of crappy but in that nice Philippine sort of way :-))  We like the view of Manila Bay from the veranda and the breakfast buffet is not bad (great fresh pandesal!).
Thanks to Hum for Coral Cay and Bethel recommendations!
Jim