hh, I lived in Northern Thailand for 15 months and also went to Cambodia and Vietnam. My sister went to Laos so I know a bit on that too. Regarding malaria, just bring the pills that you are supposed to swallow if you start feeling woozy. Don't take the stuff that you have to take every day regardless of how you are feeling; that stuff has side effects. If you bring some mosquito repellent (preferably DEET) and the anti-malaria pills that you only take when feeling symptons, then you'll be fine.
Hope you make it to Angkor Wat in Cambodia. The tourism crush is hitting it pretty hard. Beaches are better in Thailand than in Cam. You can fly straight into Siem Reap from Bangkok on Bangkok Airways, a very good airline. For where you are thinking about going, you may want to google "Bangkok Airways" and check out their airpass.
For Laos, you may want to take a boat down the Mekong from the Golden Triangle to Luang Prabang. My sister did that and liked it. LPrabang is great supposedly as is Vang Vieng. Vietniane is a bit dry.
In Vietnam, spend more time in Hanoi than in Saigon. It has more charm. See if you can make it to Sapa or Mai Chau. Rent a bike and go for a bike ride in Hanoi. Near Hue, check out the tunnels along the DMZ. Hoi An is a great place to buy clothing. My favorite beach in VN: Lang Co near Hue.
Enjoy Thailand. Check out Nan and Pai in the North. For Southern Thailand, see if you can make it to Koh Tarutao National Marine Park - most pristine beach in Thailand. Also, take an overnight train in Thailand; just be sure to buy your ticket from someone behind an official counter (and not in the lobby). The beds on the train are cheap and very comfortable. You will have to buy your ticket a day or two in advance.
Check out these Frommers links: they have all of their guidebook content online for free. I suggest the places that get more stars than dollar signs:
http://www.frommers.com/destinations/cambodia/
http://www.frommers.com/destinations/si ... nddin.html
http://www.frommers.com/destinations/si ... ndacc.html
http://www.frommers.com/destinations/vietnam/ - pay close attention to the section that says "Best of Vietnam" (a lot of good tips here)
http://www.frommers.com/destinations/vi ... 20001.html
http://www.frommers.com/destinations/vi ... 20119.html
http://www.frommers.com/destinations/laos/
http://www.frommers.com/destinations/vangvieng/
http://www.frommers.com/destinations/luangprabang/
http://www.frommers.com/destinations/thailand/ - see "The Best of Thailand" section
http://www.frommers.com/destinations/th ... 20855.html