Migrating MSMQ applications from 32-bit to 64-bit systems shouldn't be a big deal.
In theory you will probably be able to just recompile / redeploy as the public MSMQ APIs are not architecture-dependent. Other parts of your own code may be, though, so make sure you check the Getting Ready for 64-bit Windows MSDN article to learn about pointer usage rules and new data types.
Also the MSMQ message format doesn't change so you can send between different architectures without worry. It is more important to note message format differences between operating systems than between hardware archirecture.
Everything is not perfect in the garden, though, as there are some old MSMQ utilities that are not designed to run on 64-bit. For examples:
There have also been some minor bugs relating to 64-bit architecture:
And some features are not supported:
I'll add more to the blog post as I find it.