The motion of magnetic vortices in Josephson junctions is exploited in various superconductor device applications. I discuss the collective phase dynamics in conventional long Josephson junction (LJJ) stacks and in high temperature superconductors, exhibiting intrinsic LJJ behaviors. Using a theoretical model that accounts for both the magnetic induction effect and the non-equilibrium effect, I discuss how the collective motion of Josephson vortices in an intrinsic LJJ stack is modified from a conventional LJJ stack. I discuss how this modification of collective dynamics affects the application of high temperature superconductors as tera-hertz oscillators.