We report the synthesis of a new nanocrystal (NC) mesophase through self-assembly of water-soluble NC micelles with soluble silica. The mesophase comprises gold nanocrystals arranged within a silica matrix in a face-centered cubic lattice with cell dimensions that are adjustable through control of the nanocrystal diameter and/or the alkane chain lengths of the primary alkanethiol stabilizing ligands or the surrounding secondary surfactants. Under kinetically controlled silica polymerization conditions, evaporation drives self-assembly of NC micelles into ordered NC/silica thin-film mesophases during spin coating. The intermediate NC micelles are water soluble and of interest for biolabeling. Initial experiments on a metal-insulator-metal capacitor fabricated with an ordered three-dimensional gold nanocrystal/silica array as the "insulator" demonstrated collective Coulomb blockade behavior below 100 kelvin and established the current-voltage scaling relationship for a well-defined three-dimensional array of Coulomb islands.