Luke, it really depends on how long you have.
My preference is by plane because it means you get to your destination sooner (and spend logner there enjoying it) .
If you have some time on your hands, consider travelling by bus. You get to stop at smaller towns and probably see a lot more than you would in a train or plane. about 7 years ago
I'd suggest bus an ferry across Indonesia because there are so many islands to see. Then it'd be cheap flights to get to Thailand or across to Vietnam. But once in-country, I'd generally use busses. The exception is when you go say from Hanoi to Danang A then use local flights.
You have to balance the time you have (flying is faster and easier) with great local experiences. We've often found these from bus journeys because you can't always quite plan where you'll be when which means sometimes, just occasionally, you get lucky!
Enjoy about 7 years ago