Hi Gabriel -
Peninsular Malaysia has decent diving at its east coast, look up the reviews for spots like the Perhentian Islands, Redang Island, Aur and Tioman. I got certified on the Perhentians which was a lot of fun. However, having dived around in the SEA area more, I'd think there are better places. East Malaysia (Sipadan, Mabul, Layang Layang - the first two in the southeast, and the latter to the north of, the coast of Borneo) has world class spots, but this is all resort based diving - not a budget thing, if that is what you are looking for.
The Philis have budget written all over them. Little tourism, friendly people, not too special food (as compared to Indo / Thai kitchen), great dive spots. There is various options: Palawan, the Visayas (notably Moalboal on Cebu, Apo Island of Dumaguette on Negros, Alona Beach on Bohol, Malapasqua Island on the northern tip of Cebu (tresher sharks!), South Leyte). There is great diving at all these places: just search the board for spots like Pescador Island, Apo Island, Basicalag, Cabilao, Gato Island. The really good thing about the Visayas is that all spots are quite close so you can travel around and dive them all in say a month - and if you want to stay longer, accomodation is cheap.
Let me know if you want further info on these places in the Visayas. Sure you will find a lot of information on the board, do a search - you'll be amazed by the amount of info out here.
Cheers - Arie