You can use anything that will generate STL files to create things to print with a Reprap. Using something simple and open source for actual Darwin design and construction helps ensure the whole toolchain is replicable, using something written in Java helps ensure the toolchain is portable.
But once you have a Reprap, you should definitely use whatever 3D modeling tool you have available to you and are comfortable with, to generate more STLs to feed your hungry Reprap :-)
MeshLab seems to be for cleaning up existing files, not generating new ones from scratch. Useful, but not a general purpose modeling tool.
Jonathan