Because the mysql bin directory is now version dependent, there should be something that specifies what is the current version being run. This same version selector utility should also update an environment variable or optionally the PATH env. var. to allow batch files to automatically pick up the current version being run.
Something like WAMP_MYSQL="C:\wamp\bin\mysql\mysql5.0.51a" would be helpful.
I'm guessing you are working on a multiple version selector due to the new directory naming convention.