I'm a bit embarrassed :)

The protobuf version of my code uses about 950MB of memory (the Java
Serializable version is only using around 650MB) and I had the java -
Xmx flag set too low; in reality protobuf is extremely fast compared
to Java Serializable:

Java Serializable:
12,000 msgs/sec

Protocol Buffers (as described in my first post):
70,000 msgs/sec

Protocol Buffers (CodedOutputStream, as described in Evan's post):
73,000 msgs/sec

Protocol Buffers (CodedOutputStream, but no flush() after each write):
76,600 msgs/sec

Thanks very much for the help, I'm very happy with the performance!

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