Are there any chemists here? I've got something for you: My multiple bonds Demonstration is now also available as a package.
You can plot molecules from ChemicalData[] or from your own MOL files. The source only needs to contain information about the positions and multiplicity of the bonds, and of course about the positions and types of the atoms.
Here are a few examples of the finished result (the package itself contains more notes about the technical aspects).
Needs["multiBondPlot`"]
Multicolumn[Labeled[multiBondPlot[#],#]&/@{"Benzene","Caffeine","Acetonitrile","TNT"},2]
