What visa options and travel itineraries should I consider for a long trip in Thailand and neighboring countries?

Unless you use a visa agent, there is no one place to organize visas. That said, not hard to do it yourself. Laos and Cambodia offer 30 day visa on arrival and Vietnam has a 90 day eVisa. You don't need a visa for Thailand unless you plan on staying in Thailand longer than 60 days at a time - 30 day visa exempt + a 30 day extension. Not sure how Cambodia and Laos work for longer stays - visas are probably available but you may not want to stay in either for more than a month.

The fact it's a long trip and you'll likely be out of Thailand for quite a long time before re entering. I'd personally get a 60 day visa to start and get a 30 day extension and travel 90 days in Thailand first. If you were going in and out of Thailand regularly then the metv would have been perfect but I'm guessing you'll be many months in Cambodia, Vietnam and Laos so it would only make sense if you travelled 4 months in those 3 countries and re entering Thailand right at the end of the metv but I'm sure you'll want more time than 4 months in those other 3 giving the duration of your adventure.

So that's my advice. When re entering Thailand at the end just get a 30 day visa exempt. You can extend that for 30 days as well.

Sounds like a wicked journey though. Have a blast man

Switch Laos, and Vietnam in your order. Thailand, Laos, Vietnam, Cambodia, or the reverse. Then you are not entering any country more than once, except Thailand twice. Now, here is an itinerary you might consider. Enter Thailand. When you are ready to travel on go to Chang Kong in Northern Thailand, and cross over into Laos. Just down from the bridge is the slow boat down the Mekong for two days, with an overnight at Pak Bien, and on to LuangPraBang. Spend a few days there then travel down to Vang Vien, and spend how ever long you want there. From there take the buses to Hanoi, and over to HaLong bay. Back to Hanoi, and buy a cheap 125cc motorbike, and drive to HoCheMin city in the south of Vietnam. The seller will give you the address to buyer of the motorbike when you get there. Most take about a month traveling down through Vietnam this way, with lots of side excursions. From there travel to Cambodia, and Phnom Penh to start. Siem Riep is the Ankor Wat area. Cross back into Thailand, but NOT at PoiPet, as you could get hassled extensively there. Travel to Koh Chang island in Thailand after you cross back into Thailand, and spend some pure relaxation and refreshing time at Lonely Beach, or White Sand beach, whatever fits your lifestyle. Back to Bangkok and fly home. Save the next trip for the Southern islands, like Phuket, Samui, and such, unless your timing works out, and you want to hit the full moon party on Koh Pangnan. This is fitting your time frame pretty well, and you'll have no visa problems, just getting visas, or visa exempt, at the borders.

Only Vietnames bikes allowed into VN, other bikes will require tons of paperwork and guide.