Another vote for Tulamben Bali - Puri Madha has budget accommodations $10 per night - just west of the public dive park. Beautiful shore diving - bring a buddy.
Padangbai Bali - find a small budget room Toppi Inn is nice, and check dive prices with dive shops
Shore diving at Pulau Weh Sumatra, budget rooms available in the village. It's shallow but beautiful. I found the boat dives and operators quite questionable
Apo Island PI - beautiful, Try Liberty Lodge. If you don't mind roughing it inquire about home stay in the native village
Puerto Galarea PI - budget rooms can be found for $7 a night during off season. Keep looking

Try behind Action divers in small lagoon
Coron PI, budget accommodations are available in the village - dive with Discover divers
Bunakan Sulawesi - stay at Lorenzos II - dive with Living Colors
Lembeh - two fish/NAD aren't too expensive and worth visiting
Google lonely planet "thorn tree forum" for more budget travelers info
Have fun!