Maybe this
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>${mainClass}</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>${assemblyRef}</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
and invoke maven with parameters -DmainClass=my.stuff.Main1 -DassemblyRef=-main1
For making this easier to use, create profile
<profiles>
<profile>
<id>main1</id>
<properties>
<mainClass>my.stuff.Main1</mainClass>
<assemblyRef>-main1</assemblyRef>
</properties>
</profile>
<profile>
<id>main2</id>
<properties>
<mainClass>my.stuff.Main2</mainClass>
<assemblyRef>-main2</assemblyRef>
</properties>
</profile>
</profiles>
and invoke maven with parameter -Pmain1
.