We report a simple synthetic route based on electroless deposition (galvanic displacement) and natural lithography to simultaneously control the shape and organization of Au nanoparticles (NPs). We show for the first time the formation of organized extended domains of Au nanoflowers and nanocrowns with single crystalline tips. The dimension and morphology of the desired nanostructures (NSs) can be tuned easily by controlling the deposition conditions at room temperature using saccharin as an organic additive. The exact role of saccharin on the crystal growth process of Au NPs is also discussed. A systematic surface enhancement Raman spectroscopy (SERS) study of large, ordered areas of organized gold nanoflowers using p-mercaptoaniline (pMA) as the probe molecule shows massive and reproducible enhancements of the Raman signal. By comparing the relative enhancement of the different vibrational modes as a function of the morphology, the specific charge-transfer (chemical effect) SERS mechanism can be distinguished from the general electromagnetic field enhancement (physical effect). A wide range of applications can be envisaged for these SERS substrates.