We have characterized the terahertz (THz) vibrational spectroscopy of organic polycrystalline thin films using the new experimental technique of waveguide terahertz time domain spectroscopy (waveguide THz-TDS). The organic materials used in this study are tetracyanoquinodimethane (TCNQ) and 1,3-dicyanobenzene (13DCB). For each material, a thin film is cast onto one of the inner surfaces of a metal parallel plate waveguide (PPWG), followed by measurement of the low-frequency vibrational spectrum using waveguide THz-TDS. The vibrational spectra of the waveguide films are compared to corresponding vibrational spectra of standard pellet samples made by dispersing the organic solid in transparent polyethylene. We show how the waveguide films produce significantly narrower THz vibrational line shapes and reveal additional spectral lines that are obscured by inhomogeneous broadening effects in the pellet samples. When TCNQ waveguide films are cooled to 77 K, vibrational line widths as sharp as 25-30 gigahertz (0.83-1.0 cm(-1)) at the full width at half-maximum are observed, which are among the narrowest far-infrared line widths measured for this material. The origin of the line-narrowing effect for the waveguide films is the suppression of inhomogeneous broadening due to the planar ordering of the film on the waveguide surface. The TCNQ waveguide films are further characterized using optical microscopic evaluation to understand how film morphology affects the THz vibrational spectrum. X-ray diffraction is used to determine the orientation of the polycrystalline TCNQ films on the PPWG surface and to qualitatively explain the different vibrational line strengths observed for the ordered waveguide film relative to the random pellet.