Waves that propagate between the outer magnetospheric regions (in particular the magnetopause or the magnetotail) and the ionosphere and thereby mediate the dynamic processes of the magnetosphere-ionosphere-thermosphere system are affected at the lower end of their paths by the interaction of the plasma with the neutral atmosphere. We use three-fluid equations (electrons, ions, and neutral particles) to study wave propagation and derive the general dispersion relation, under the simplifying assumptions of incompressible parallel propagation in a locally uniform system. Included are the effects of ion-neutral, electron-neutral, and ion-electron collisions on the electric current and on the plasma flow, as well as the effect of plasma-neutral collisions on the neutral atmospheric flow. At low frequencies, near and below the ion-neutral collision frequency, the properties of propagating perturbations are modified as a result of the interaction with the neutral atmosphere. Because the wavelengths may be too long for the local-uniformity assumption to apply, the quantitative statement of the modifications may not be reliable, but their qualitative properties are clear. Wave speed becomes substantially slower than the Alfvén speed because of inertia loading by neutrals. Waves are significantly damped because of plasma-neutral friction. Left-handed and right-handed waves have different dispersion properties because ion motion is inhibited much more than electron motion by collisions with neutrals. At still lower frequencies, below the neutral-ion collision frequency, plasma and neutrals move together, leading to wave speed equal to the Alfvén speed based on the total (plasma plus neutral) mass density and to disappearance of damping and of differences between left-handed and right-handed dispersions. These results indicate that the coupling of ionosphere and neutral atmosphere is better described as a (frictional) neutral-drag process rather than as Ohmic dissipation, in agreement with the conclusions of another direct study of energy equations in the ionosphere-atmosphere system.