This work explores the capability of simulating complex fluid flows by directly solving the Boltzmann equation. Due to the high-dimensionality of the governing equation, the substantial computational cost of solving the Boltzmann equation has generally limited its application to simpler, two-dimensional flow problems. Utilizing a combination of high-order spatial discretizations and discretely-conservative velocity models along with their highly-efficient implementation on massively-parallel GPU computing architectures, we demonstrate the current ability of directly solving the Boltzmann equation augmented with the BGK collision model for complex, three-dimensional flows. Numerical results are presented for a variety of these problems including rarefied microchannels, transitional and turbulent flows, and high-speed atmospheric re-entry vehicles, showcasing the ability of the approach in accurately predicting complex nonlinear flow phenomena and non-equilibrium effects.