Since the last decade, nanohole arrays have emerged from an interesting optical phenomenon to the development of applications in photophysical studies, photovoltaics and as a sensing template for chemical and biological analyses. Numerous methodologies have been designed to manufacture nanohole arrays, including the use of focus ion beam milling, soft-imprint lithography, colloidal lithography and, more recently, modified nanosphere lithography (NSL). With NSL or colloidal lithography, the experimental conditions control the density of the nanosphere mask and, thus, the aspect of the nanohole arrays. Low surface coverage of the nanosphere mask produces disordered nanoholes. Ordered nanohole arrays are obtained with a densely packed nanosphere mask in combination with electrochemical deposition of the metal, glancing angle deposition (GLAD) or etching of the nanospheres prior to metal deposition. A review of these methodologies is presented here with an emphasis on the optical properties of nanoholes interesting in analytical chemistry. In particular, applications of these novel plasmonic materials will be demonstrated as substrates for a localized surface plasmon resonance (LSPR), Surface Plasmon Resonance (SPR), surface enhanced Raman spectroscopy (SERS), and in electrochemistry with nano-patterned electrodes.