If you are backpacking 'round the world, here are some great SE Asian spots for good times underwater and on land. Of course, all this is contingent on season. Hope this helps. Have a great trip!
-Hapadiver
THAILAND
Koh Tao: Cheapest in Thailand. Party island. Much, much cheaper accommodation than Koh Samui, which is a resort town. Besides, there's no diving off Koh Samui. They ruined the reefs. All the "good" diving is done off Koh Tao or Ang Thong Marine Park, which can also be dived from Koh Tao. Koh Tao is a good place for the beginner. People who've done a lot of diving will be far less impressed.
Koh Lanta: West coast. Has better diving. Little more money but worth it. All shops dive the famous Hin Daeng (Red Rock) and Hin Muang (Purple Rock). Lanta Divers is an excellent company. Stay on Long Beach. Best for backpackers. Most fun. Nicest beach. Another good reason to stay there is that the west coast desperately needs tourists to return after the tsunami. It's a beautiful island, which did not receive the kind of damage that Phuket and Phi Phi did. Most of it has been repaired by now.
MALAYSIA
Perhentian Islands: The diving is lovely here. There's a nice variety of sites, including two wrecks. It's very affordable, though accommodation is a bit pricier in Malaysia than it is in Thailand. Had the opposite season. Shuts down during monsoon. Stay on Pulau Kecil (Small Island), on long beach. This is one of the prettiest beaches I've seen in SE Asia. It's also the most fun. Spice Divers is an excellent company.
INDONESIA
Gilli Trawangan: This is a good place to take an advanced course. It's very affordable. It's loads of fun. You can also get the scoop on ultra cheap liveaboards. And, once you're advanced, you can head back to Bali or any of Indo's other fab dive locales for some wicked diving. Blue Marlin is an excellent, well-run dive shop. Like Koh Tao, this is a good place for instruction but not the most amazing dive spot in the world. Though coral is only good in deeper sites, you'll still see loads of sharks and turtles on most every dive.
Komodo: Not sure how adventurous you are, but if you are planning on heading into eastern Indonesia, Komodo is a must-see. Had the best dive of my life there -- too many manta rays to count. All the diving is done from Lubuanbajo, which is on the western tip of Flores. Komodo is also pretty affordable, when dived from Lubuanbajo. People shell out major cash to dive this region from Bali-based liveaboards. Reefseekers was an amazing company. Two of the best DM's I've ever had.
Togean Islands, Sulawesi: If you have A LOT of time and will power, then don't miss the Togean Islands. This place is island paradise defined. Beautiful reefs, fish, beaches, sunsets ... It takes two days to get there from any direction. The diving is CHEAP. Accomodation is simple but absolutely beautiful. Cost is about $7 to $10 US a day. This includes meals. The diving is beautiful. You will never, never want to leave. Black Marlin is the best dive shop. It's on the island Kadidiri. I liked this place better than famous Bunaken.
Lembeh Straits, Sulawesi: Once you've perfected your buoyancy, head here for some killer muck diving.
VIETNAM
Nha Trang: The diving here is pleasant. The beach is beautiful. There are many, many dive shops to chose from. Depending on the time of year, the water may be a wee bit cold. It's a little pricier than Thailand, but if you are already in Vietnam, then why not dive there?