These are places I'm familiar with. I can't imagine a $1000 room, but then I've always been poor so I don't miss it. Also if you are looking for inexpensive, ignore the "Super Deluxe Room Rate" and look at standard. Also really cheap places aren't going to be easy to find on the Internet, but surprisingly quite a few are. Remember that most of the posted rates are in Pesos, with an exchange rate of roughly 50:1.
I've gone here several times, before they had high speed internet, or dependable phone service, but they do advertise having those now. Roughly $20 for a standard room
Malapascua
This is the place closest to my house on cebu, about an hour drive over the mountains
Moalboal
I've got to throw this one at you, since it isn't included in the above list. We had reservations at another hotel, walked down the beach, and saw this place. Asked about it and immediately moved all our stuff here! The president of the Philippines stays here when she comes to Moalboal, and it's $100/night. That's a lot for me, but the people treated me like the president! Best part , we were there in July and were the only people staying there! Fantastic place. I just booked a business room in a nearby large city in U.S., the accomodations are nice, but it's $200/night! To think I could stay two nights in Club Serena for the same price!
Siquijor Island is really nice, somewhat remote with lots of good small places to stay. Divings great, people especially friendly, prices very reasonable. If I could afford a second house in the Phils, it'd be here, so far.
Siquijor Island