Resignator
The full source code is availble on GitHub here.
To download the app, follow the link below to the Java WebStart JNLP file. You'll need a JDK (not a JRE) installed as this app makes use of the keytool and jarsigner executables.
This will download the .jnlp file on your machine. You'll need to visit the Downloads folder of your browser and make an addtional selection to actually run the app. Subsequent executions will have a shortcut available.
I use Resignator for two use cases. Sometimes, I have a folder of unsigned third-party JAR files that I need to sign. I create a pair of folders "signed" and "unsigned". I add the JARs to the unsigned folder and run Resignator. The signed files gather in the signed folder.
The second use case involves working with third-party JARs that are updated frequently. These JARs aren't part of my build process, so they don't get the jarsigner treatment in my Maven files. When I get an updated JAR -- say a SNAPSHOT build -- I put it into a known location and run Resignator. Resignator puts the signed JAR in the target folder.
In the past, I've used Ant scripts to do this type of JAR signing. I think you'll find this more productive because of all your signing operations will be just a click away. You won't have to go to the command line and maintain a set of scripts.