www-client/chromium-9.0.597.19 compiles bundled protobuf, it's available as dev-libs/protobuf.
Last summer I tried to unbundle it, but it's not trivial. The bundled copy of protobuf is modified so that it's incompatible with dev-libs/protobuf. I think it should be fixable, but with more upstream effort.
Fixed in chromium-25.0.1349.2 . Isn't that cool? ;-)
Nice! And it only took 2 years and 16 releases. :P