You can do it. You'll need a separate execution for each artifact that you're building (i.e., give each its own id but you can leave the phase as default), and you'll need to specify the finalName and archive/manifest/mainClass for each.
maven-assembly-plugin
build-a
foobar.Aclass
jar-with-dependencies
foobar_a.jar
build-b
foobar.Bclass
jar-with-dependencies
foobar_b.jar