I can only help you with Thailand and Cambodia so far (I'd be able to help you some more by now if I hadn't hit a cambodian water buffalo and broken my arm).
Anyway, Thailand do not operate a carnet scheme. Instead they make you sign a declaration (called a Simplified Customs Form) stating that you will pay 500,000 baht (which I believe is the standard price for motorcycles) - about 11,000USD - if you don't re-export the bike within 28 days (even if you have a 60 day visa). However, that was flying the bike into Bangkok airport. When leaving Thailand to Cambodia the Thai officials had never heard of the form. They kept looking at my copy in bewilderment and asking for my carnet. It was only after explaining the situation to them several times that they found the right form for export. So be prepared for anything if you are entering from Malaysia. Personally, I would offer them the carnet if you have one - it beats paying over 11,000USD if the bike is stolen.
In Cambodia they don't seem to bother which any such formalities. I had no paperwork at all for the bike when I entered at Poipet from Thailand.