Here's my rundown. I live in Japan now and also did so back in the mid nineties, and have had a chance to pop all over the place.
A lot depends on your timing. If you're backpacking, Seoul is friggin cold right now, so you'll need winter stuff which you may not want to drag along. (Japan isn't as cold as Korea but you still need a jacket). Summers are disgustingly hot across the region no matter where you go, so if you plan your trip for late March/April/May you'll do doing yourself a favour.
Here's a rundown.
Hong Kong - hub for flights in SE Asia, and a blast to visit. Expensive, but with good sanitation and trustworthy restaurants & drinking water its nice to come back to. Some of the best eateries in the world.
Philippines - Nice scuba diving. Transportation and getting around is an absolute gong show. We tried to travel around but buses and boats were so haphazzard, we wound up sticking in one lovely spot, drinking and diving for two weeks (which was a blast). Manilla is a horrible town, but has a casino that I won $300 at.
Vietnam - Wicked place, though I imagine it's changed in the 10 years. Cheap, reasonable transportation (not too hard to get top to bottom) good food and lots to see in the south. Hanoi was a little stoic and cold but if you can visit Hue, Nha Trang and the Mekong delta.
Laos - Drug capital of Asia - so much dope and opium it will spin your head. Impossible place to get around in, and one of the poorest places in the world so, like the Philippines - pick a spot and stay there. Nice, nice, nice people.
Burma - I don't support the junta so I cancelled my trip there.
Thailand - Very good food, decent transport, nice beaches and lots of things to do. Avoid the West Side of the Country right now (for obvious reasons) and stick to the islands in the east and Chang Mai, etc, in the north.
Malaysia - Go to Tioman Island. The most beautiful place I've been to on earth, I think. It's where they shot the movie South Pacific. Easy to get around in, good food and KL is a fun city.
Singapore - I liked having Singapore Slings at Raffles hotel (I had a 10 hour layover so my buddies and I just went into town for a drink). Other than that it was a good place to cool my heels while waiting for my friends before we went to Indonesia. Saw movies and ate Indian.
Indonesia - I loved Indonesia back in 1994. Lord knows, there has been a number of things that might have changed the situation there (increased Muslim hostility to outsiders, terror, etc) but Jojyakarta and the surrounding ruins, Ceylon, Bali, Lombok and the islands were pretty good and pretty fun. Lots of Aussies in Bali, too (sorta like there are lots of Canadians in Mexico) so it's almost like being in Australia. This would be a good way to get to Austraila, though. Watch the water, though - my buddy got super ill in Indonesia when he bought some "bottled" water that was from a tap (once it cooled down we noticed the smell and the illness countdown begun).
I haven't been to Korea or mainland China outside of Shanghai (and I was only there for a day) so I can't comment but like Fotze said - Lonely Planet is your bible for this kind of trip. Hostels are cheap, but the quality varies widely depending on the country. If you can, book a night or two at a hotel (Holiday Inn or something) until your body shakes off the jetlag at your first destination in SE Asia.
Oh, and if you're planning on coming to Japan, bring lots of money. What's your daily budget, anyhow?
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