The enhancement of fluorescence and Raman scattering by plasmonic nanostructures is studied theoretically with special focus on the effects of the observed molecule's properties and the realistic geometry of the plasmonic nanostructure. Numerical experiments show that the enhancement factor may vary by many orders of magnitude depending on a fluorophore's transition rates or intrinsic quantum yield. For different molecules, boosting fluorescence enhancement means optimizing different factors, leading to a different ideal geometric and spectral configuration. This framework, coupled with powerful new simulation tools, will facilitate the design and characterization of fluorescence-enhancing plasmonic nanostructures as well as yield experimental access to the intrinsic properties of the molecules under study.