I never implemented anything using boost's library, but I found Google protobuff's to be more thought-out, and the code is much cleaner and easier to read. I would suggest having a look at the various languages you want to use it with and have a read through the code and the documentation and make up your mind.
The one difficulty I had with protobufs was they named a very commonly used function in their generated code GetMessage(), which of course conflicts with the Win32 GetMessage macro.
I would still highly recommend protobufs. They're very useful.
