At the core of photoluminescence techniques are suitable fluorescent labels and reporters, the spectroscopic properties of which control the limit of detection, the dynamic range, and the potential for multiplexing. Many applications including recent developments in intracellular labeling rely on well established molecular chromophores such as small organic dyes or fluorescent proteins. However, one of the most exciting -but also controversial -advances in reporter technology, the emerging development and application of luminescent nanoparticles with unique optical properties, yet complicated surface chemistry paves new roads for fluorescence imaging and sensing as well as for in vitro and in vivo labeling. Here, we compare and evaluate the differences in physico-chemical properties of common fluorophores, focusing on traditional organic dyes and luminescent nanocrystals with size-dependent features. The ultimate goal is to provide a better understanding of the advantages and limitations of both classes of chromophores, facilitate fluorophore choice for users of fluorescence techniques, and address future challenges in the rational design and manipulation of nanoparticulate labels and probes.