The quasi-particle energy spectrum of the Hartree-Fock-Bogoliubov (HFB) equations contains discrete bound states, resonances, and non-resonant continuum states. We study the structure of the unbound quasi-particle spectrum of weakly bound nuclei within several methods that do not rely on imposing scattering or outgoing boundary conditions. Various approximations are examined to estimate resonance widths. It is shown that the stabilization method works well for all HFB resonances except for very narrow ones. The Thomas-Fermi approximation to the non-resonant continuum has been shown to be very effective, especially for coordinate-space HFB calculations in large boxes that involve huge amounts of discretized quasi-particle continuum states.