We present a study of the effects of inelastic scattering on the transport properties of various nanoscale devices, namely H2 molecules sandwiched between Pt contacts, and a spin-valve made by an organic molecule attached to model half-metal ferromagnetic current/voltage probes. In both cases we use a tight-binding Su-Schrieffer-Heeger Hamiltonian and the inelastic effects are treated with a multi-channel method, including Pauli exclusion principle. In the case of the H2 molecule, we find that inelastic backscattering is responsible for the drop of the differential conductance at biases larger than the excitation energy of the lower of the molecular phonon modes. In the case of the spin-valve, we investigate the different spin-currents and the magnetoresistance as a function of the position of the Fermi level with respect to the spin-polarized band edges. In general inelastic scattering reduces the spin-polarization of the current and consequently the magnetoresistance.