I present a broad overview of the current cosmic-ray (CR) transport modeling, and discuss several recent results obtained with the DRAGON code. Several anomalies in the measured CR spectra and gamma-ray data are discussed with particular focus on: the positron excess, the hint of an antiproton excess, the proton and helium spectral breaks, the gamma-ray GeV excess, which may point to either new classes of sources, non-standard propagation models, or new physics.