We recently had a situation where a consumer had mismatched the runtime: one version of cordova.js and another version of the Cordova native code. The consumer gave us their compiled app, so we didn't have access to the native's source in the project. We had an idea that it would be nice if the native code compiled in some marker so we could tell what version it was without the source. Perhaps issue a log on startup saying "Greetings from Cordova native code 3.2.0", or have something compiled in that would appear in "strings cordova.jar | grep version".
See some discussion at http://markmail.org/thread/m4h4csvcq4cs3dcr