While DNA sequence evolution is well studied, the evolution of gene expression is currently less understood. Though there exist theoretical models to study the evolution of continuous traits such as gene expression, these methods often cannot confidently distinguish alternative evolutionary scenarios, probably, due to the modest numbers of species studied. We hypothesized that biological replicates could increase the predictive power of these models and accordingly developed EvoGeneX, a computationally efficient method based on the Ornstein-Uhlenbeck process to infer the mode of expression evolution. Furthermore, we used Michaelis-Menten equation to compare the evolutionary dynamics across groups of genes in terms of asymptotic level and rate of divergence. We applied these new tools to preform the first ever analysis of the of expression evolution across body parts, species, and sexes of the Drosophila genus. Our analysis revealed that neutral expression evolution can be confidently rejected in favor of stabilizing selection in nearly half of the genes. In addition, neutrally evolving genes evolve fastest in male gonads and faster in female gonads than other body parts. The gonads also have the largest sets of unique adaptive genes. We also detected interesting examples of adaptive genes including Glutamine Synthases and odor binding proteins.