I've played around a little with both systems, nothing serious, just some simple hackish stuff, but I felt that there's a real difference in how you're supposed to use the libraries.
With boost::serialization, you write your own structs/classes first, and then add the archiving methods, but you're still left with some pretty "slim" classes, that can be used as data members, inherited, whatever.
With protocol buffers, the amount of code generated for even a simple structure is pretty substantial, and the structs and code that's generated is more meant for operating on, and that you use protocol buffers' functionality to transport data to and from your own internal structures.
