Vietnam: Risk of malaria in the whole country except urban area's, Red River Delta and coastal plains north of Nha Trang. Recommended prophylaxis: mefloquine, or doxycycline or atovaquone/proguinal.
Cambodia:Risk of Malaria throughout the whole country except Phnom Penh. Rec. Prophylaxis, same as Vietnam but mefloquine not suitable for Western Border Area's
Thailand: No risk in the cities or main touruist areas. Long stays in rural area's with forests, and in border areas with Laos, Mynamar or Cambodia, doxycycline or atovaquone.
Don't forget non pharmaceutical measures (avoiding getting bitten).
You really need an expert "risk assessment" by a travel clinic / specialist, if you are travelling for a while in local conditions. You may need more than the "bog standard" hep a + typhoid jabs. I suggest you contact an AME to discuss which drugs mix with flying, prior to going to the travel clinic. (As there is a choice of drugs available).
Also read "Health Advice for Travellers" available from the post office.