I would like to hire a trail motor bike from hanoi, vietnam and ride it
through laos, cambodia and leave in in bangkok, thailand. Are there
any companys which will do this sort of cross country hire? If so what
are they? (I leave Australia christmas day for 3 weeks) Would this
mode of transport be ok at the border crossings?

Your best bet would be to buy a second-hand bike in Hanoi and then
sell it when you get to Bangkok.

You shouldn't have any problems with border crossings as long as you
have the necessary visas.

For more information check out The Minsk Club in Hanoi:

http://www.minskclubvietnam.com/TheClub.html

Here is another site that you should find interesting:

http://www.horizonsunlimited.com/ubb/Forum33/HTML/000031.html

Click on the topics at the left.  I found this looking for "carnet de
passage", which can read about there.  Here it is explained in more
detail:

http://www.spiritsofadventure.com/links/international_driving_permits_an.htm

If a carnet will be necessary, obviously it will have to be secured in
Vietnam, but maybe the people at "Minsk" can advise and possibly
assist you.

If one is required for bringing a bike into Thailand, this could be a
problem if you try to sell it there, besides the difficulty of
spending your last days in Bangkok just trying to market a bike.  IF
it had been brought in on a carnet, and if the Thai authorities got
their act together, they would get back to the issuer of the carnet
and ask for import duty.

This site seems rather discouraging:
http://bptravel.tripod.com/vechimpt.htm

Here is another one that offers information.  

http://dg.ian.com/index.jsp?cid=54608&action=viewLocation&locationId=27944

Click on Overland routes and Entry requirements.

I seriously doubt that it is possible to rent a bike in Vietnam and
"return" it in Thailand.  A rented bike would still present all the
border problems that your own would.
But who knows?  I don't want to put a damper on your plans.
Myoarin

i feel travelling over land to all the nations is not a problem
,infact recently about four or five months ago only a car rally was
organised from india to some where in hanoi to show that overland
route traversing through all these nations is possible. if you have a
valid license and if some body is willing to vouch for the fact that
the vehicle that you are driving is not stolen then driving with a two
wheeler poses no problem.

I have lived in Vietnam for 8 years, and have rented and ridden trail
bikes in Cambodia. I would suggest that you go country by country
rather than trying to go from Hanoi to Thailand. I was in Cambodia in
February, and at that time you could travel freely between Thailand,
Cambodia and Laos  ( on a bike with proper papers), but not into
Vietnam.

Rent a bike in Hanoi, drive it down to HCMC and then sent it back up
on the train. The bike shop you rent from in Hanoi should be able to
pick it up. Then, cross over to Cambodia by bus ($7 or $8, takes 5 or
6 hours) or by plane. Rent a bike in Phnom Penh. You could then ride
from Phnom Penh up Angkor Wat, crossing into Laos and then, if you had
the stamina, keep going into Thailand.

As you don't have much time, I would suggest just doing Vietnam,
Cambodia and Laos, and skipping Thailand. Do Vietnam as suggested.
Rent a bike in Phnom Phen (easy to find a rental place in guidebooks
and on the internet), head Northeast towards Krabi, continuing North
into Laos, riding through Laos, and looping  back down to catch Angkor
Wat on the way back to Phnom Penh. Drop the bike off in Phnom Penh and
then head home.

Good luck with your adventure. Drive very carefully, as the medical
facilities in SE Asia and very rudimentary, and people do not always
follow the traffic rules. But, there is a lot of beauty to see.