To me, how you keep them in source control depends on how you envision them as distributions. If all of the modules are tightly coupled and you would never want to release one without another, then you would want to have

MassSpec/lib/MassSpec/SVGIsotopeClusterGraph.pm
MassSpec/lib/MassSpec/ViewSpectrum.pm
MassSpec/lib/LipcutElementsIO.pm
MassSpec/lib/LipcutElementsIO/Search.pm
MassSpec/t/
MassSpec/Makefile.PL
[download]

etc.

If you had three separate components that could be maintained and updated separately, then you would treat them as three distributions:

MassSpec-SVGIsotopeClusterGraph/lib/MassSpec/SVGIsotopeclusterGraph.pm
MassSpec-SVGIsotopeClusterGraph/t/
MassSpec-SVGIsotopeClusterGraph/Makefile.PL

MassSpec-ViewSpectrum/lib/MassSpec/ViewSpectrum.pm
MassSpec-ViewSpectrum/t/
MassSpec-ViewSpectrum/Makefile.PL

MassSpec-LipcutElements/MassSpec/LipcutElementsIO.pm
MassSpec-LipcutElements/MassSpec/LipcutElementsIO/Search.pm
MassSpec-LipcutElements/t/
MassSpec-LipcutElements/Makefile.PL
[download]

etc. etc.

And if all four of them are envisioned as separate components then you might have four dists, but I'm guessing it's not so, and I think I've played with <code> enough for now. ;)