What we did was create a folder structure for the properties that were environment specific. Under that folder we created folders for each specific environment targeted for deployment, including local development. It looked like this:
Project
\
-Properties
\
-Local (your PC)
-Dev (shared dev server)
-Test (pre-production)
-Prod (Production)
In each folder we put parallel copies of the properties/config files and put the different configurations only in the file in the appropriate folder. The secret was to control the classpath of the deployment environment. We defined a PROPERTIES classpath entry on every server. On Prod, it would be set to "$ProjectDir/Properties/Prod" while on Test the same variable would be set to "$ProjectDir/Properties/Test".
This way we could have database connection strings for the dev/test/prod database preconfigured and not have to checkout/in the property file each time we wanted to build for a different environment.
This also meant that we could deploy the exact same .war/.ear file to Test and Prod without rebuilding. Any properties that weren't declared in the properties file we handled in a similar way by using the same JNDI name in each environment but using values that were specific to that environment.