i do not know about the boats, but you can reduce some intra asia costs by using air asia, but not to manilla....

why not just stick to SEA as a destination and go to the phillipines another time....plenty of beach locations there??

but of course over xmas the prices are at their highest of the whole year and availability might be limited....book now..

No need to take flights all the time. There are also buses from Siem Reap to Phnom Penh which would take around 5 hours. Try Mekong Express.
Spend a day or to in Phnom Penh.
From PP, there are also buses to Ho Chi Minh, which would take around 6 hours.
From HCM you can take Cebu Pacific, Philippine Airlines (both offer cheap flights) or Vietnam Airlines to the Philippines.

You will be traveling at the busiest and most expensive time of the year. I'd suggest you make your reservations as soon as you can.

There are three boats that cruise the Mekong from HCMC to Siem Reap and return. All take a week, and all are fairly expensive (about $3000-4000 per person double occupancy). There is a boat from Siem Reap to PP which is not recommended. Better to take the luxury bus or a taxi.

It sounds like you haven't fully decided on where you will be the first two weeks, but have decided on the Philippines for the third. Given travel time, you likely want to choose not more than three locations in SE Asia for the first part of your trip. You mention Chiang Mai and Siem Reap that sound firm... do you have a third location in mind? Bangkok would be the most convenient in terms of air connection. You do have to fly through Bangkok from CM to get to Siem Reap, and you'd need to fly back to Bangkok (or to somewhere else) to fly to the Philippines. Your itinerary does make logistics a bit complicated.

Thank you all for your advise.

Indeed I have realised I need to book fast so I am trying to make up my mind.

Therefore I have decided on skipping Chiang Mai this time round and instead flying to Sien Riep through Bangkok, then mtaking the bus (as suggested) to Phnom Pehn and from there making my way to Saigon. From Saigon I have booked a flight to Manila.

So the only outstanding question is how to get from PP to Saigon. I am considering taking a boat in order to see more/different scenery but not sure whether there is one direct to Saigon or I should take the ones to Chau Doc, potentialy spend a night there and then take a bus to Saigon?

Any thoughts?

Thanks,
Panlou

Check out http://talesofasia.com/ and http://www.travelfish.org/ . these sites should provide the info you need on buses/boats etc

Yes, the two websites crellston gives you will give you all you need to know about ground transport from PP to HCMC.

Remember, you must have a visa in advance to enter VN. As you are entering via land border, you'll need to get one from an embassy or consulate in your own country before you leave.

As you know, from HCMC, there are good air connections to the Philippines.