Another similar option that I think Nick briefly alluded to in the comments is to create multiple wrapper jars. I haven't tried it, but I think they could be completely empty other than the manifest file, which should specify the main class to load as well as the inclusion of the MyJar.jar to the classpath.
MyJar1.jar\META-INF\MANIFEST.MF
Manifest-Version: 1.0
Main-Class: com.mycomp.myproj.dir1.MainClass1
Class-Path: MyJar.jar
MyJar2.jar\META-INF\MANIFEST.MF
Manifest-Version: 1.0
Main-Class: com.mycomp.myproj.dir2.MainClass2
Class-Path: MyJar.jar
etc.
Then just run it with java -jar MyJar2.jar