My wife and I will be traveling to Thailand, Vietnam, and Cambodia through the summer of 2006. We are travelling from Toronto and want to have a stopover to give the least travel stress effect. Is it best to go east to west or west to east and what is the best place to stop for a sleep? (My wife has epilepsy and the full length flight is too long a stretch)

Looks to me to be about the same outbound going east or west. The difference is that going trans-pacific is that you would have one very long flight followed by a short one.

For example 16 hours to Hong Kong + 3 hours HK to Bangkok. Or 14 hours to Tokyo + 5 hours Tokyo to Bangkok.

Trans-atlantic it is about 11 hours to Munich + 8 hours from there to Bangkok.

Those are rough times for flying, not counting connection time.

New York JFK to Bangkok is 17 hours on Thai nonstop.

Returning across the Pacific looks shorter than going via Europe.

There is the choice of going westbound or eastbound. Others will tell you more about options westbound from Toronto.
If you want reasonable 'sectors' without too long in the air 'Etihad Airlines' fly 3 x weekly from Toronto-Brussels-Abu Dhabi. That gives you 2 sectors on the flight about 6.5-7 hrs each. Etihad has seatback TVs and good quality service. You then on current schedules overnight in Abu Dhabi then fly next morning to Bangkok . Onwards from Abu Dhabi to Bangkok is about 6 hrs. So that would be Toronto-Brussels-Abu Dhabi-Bangkok. Return straight through leaves Bangkok about 8 am into Toronto that night.
I believe westbounds would mainly be AC over Yancouver or whatever.

Also eastbound you have choices such as Lufthansa/Air France/KLM, that would be I guess 6.5-7 hrs into Europe but then you need to 'change planes', onwards from there to Bangkok would be non-stop and that takes best part of 11-12 hrs. So maybe the thru plane to Abu Dhabi with the option to really break up the trip with an Abu Dhabi overnighter might be nice if you prefer sectors around 7 hours as opposed to long non-stops.

From Bangkok if you are heading to Siem Reap that is just a 55 minute 'hop'. Bangkok-HCMC(Saigon) is about 1 hr 30 and Bangkok-Hanoi about 1 hr 50.
If you are going to Siem Reap in Cambodia to see Angkor Wat note that Bangkok Airways ( www.bangkokair.com ) is the only carrier. You 'can' then fly from Siem Reap to HCMC(Saigon) but that would be with Vietnam Airlines.
It really depends where you want to go in Vietnam before suggesting the best/cheapest flights. You may find it easier to fo BKK-Siem Reap and back and then do BKK-Vietnam and back, perhaps a BKK-Hanoi-HCMC-Bangkok routing.

Just to add Abu Dhabi is a fine modern city with great hotels, you will find that the airline will normaly arrange the hotel and transfers for you, the Gulf airlines are very good like that, Abu Dhabi has superb hotels and that would break up the trip nicely. Worth checking with travel agents as they certainly from Asia offer some great fares.

You can try a round-the-world ticket. [Especially if you're going business class, as a business RTW ticket doesn't cost much more than regular roundtrip.] They give you lots of flexibility in routing and stopovers.

If that's what you're doing, I suggest something like YYZ-Europe, Europe-BKK, wherever in SE Asia-Tokyo, and finally Tokyo to YYZ. And yes, an additional stop in the Gulf States will work too.

you could stop in europe for a couple of days or in the middle east or both...

going the other way you could stop in CA, WA or western canada and then in hawaii and then in japan

how about sedation??

talk to your doctor about alternatives from a medical point of view...