Porphyry copper deposits represent one of the largest copper reserves on Earth. They typically contain large, low-grade reserves of primary ore and higher-grade, supergene enrichment blankets of sulfide and oxide ores. Understanding the mineralogy of porphyry copper ores and ores related to porphyry copper systems is exceedingly important for several reasons, foremost of which are the information provided by ore mineral parageneses, assemblages, and mineral chemistry on evolution of these magmatic-hydrothermal systems, and information on mineral processing characteristics of the ores. The focus of this work is to better understand the mineralogy of supergene copper sulfides in porphyry copper systems and hypogene base metal lodes related to porphyry copper systems, and use this mineralogical knowledge to improve our understanding of the processes responsible for ore formation. The objectives of this study are accomplished by two means: focusing on the crystallography and crystal chemistry of minerals, and then applying this mineralogical knowledge to a supergene sulfide enrichment blanket and hypogene massive sulfides from base metal lodes in southeastern Arizona. The discovery of a new mineral, natropalermoite, NaSr2Al4(PO4)4(OH)4, provided the opportunity to use single-crystal X-ray diffraction to solve a crystal structure, and electron-probe microanalysis (EPMA) to study the crystal chemistry of natropalermoite and how the accommodation of Na in the structure changes lengthens the unit cell along [010] and shortens it along [100] and [001] compared to its lithium analogue, palermoite. Solution of the crystal structure of the mineral nickelskutterudite, (Ni,Co,Fe)As3, allowed for the investigation of anion deficiency in minerals of the skutterudite group, a problem whose solution has eluded researchers for nearly 100 years. Two skutterudite (CoAs3) and two nickelskutterudite samples were analyzed using single-crystal X-ray diffraction, EPMA, and procrystal electron density. The results showed fully-occupied anion sites and a cation surplus, which was accommodated in the icosahedral site, proving that minerals of the skutterudite group are not anion deficient. This mineralogical knowledge was applied to the supergene enrichment blanket in the Western Copper section of the Morenci mine, Greenlee County, and hypogene massive sulfide deposits associated with a porphyry copper deposit at Bisbee, Cochise County, Arizona. This is one of very few studies of supergene sulfide blankets ever completed. One drill hole through the supergene blanket at Western Copper was examined using ore microscopy and EPMA. Results showed dominant (Cu+Fe):S ratios of 1.80 ± 0.05, 1.92 ± 0.03, and 1.10 ± 0.10, with higher (Cu+Fe):S dominant high in the blanket and low ratios dominant near the base of the blanket. These values were interpreted to be controlled by activity of Cu2+, Fe2+, and Fe3+ in solution. Massive sulfide deposits at Bisbee were investigated using ore microscopy and EPMA in order to correct the previous conflicting reports of the mineralogy and paragenesis of this famous district and interpret constraints on conditions of ore-forming fluids. Results show four types of ore: chalcopyrite-rich with hematite and/or pyrite, bornite-rich, chalcocite-rich, and a Zn-Pb association. Chalcopyrite-rich ores formed first, followed by bornite-rich and chalcocite-rich ores. All ores were formed at relatively shallow depths from oxidized, moderately sulfur-rich fluids; early fluids were higher temperature and later fluids were lower temperature and considerably more sulfidized. Zinc-lead ores formed early and were continuously dissolved and reprecipitated distal to Cu-mineralization. These patterns are similar to many other base-metal lode districts worldwide, however Bisbee contains more Zn-Pb ore than other districts with hematite-containing ores and less than those without hematite.