We present and analyze observations–carried out using the Infrared Spectrograph (IRS) on the Spitzer Space Telescope–of the R(3) and R(4) pure rotational lines of hydrogen deuteride (HD) detected from shock-heated material associated with the supernova remnant IC 443C and with the Herbig-Haro objects HH 7 and HH 54. Assuming a continuous temperature distribution for gas observed along the sight lines, we have constrained the gas density to be in the ∼103-104/cm3 range, using both spectroscopic data for H2, HD, and CO from IRS and from the Infrared Space Observatory (ISO), as well as photometric data from Spitzer's Infrared Array Camera. The derived HD abundance relative to H2 is quite sensitive to the assumed excitation conditions in the emitting gas. Assuming that HD accounts for all gas-phase deuterium in the emitting material, and using all the available spectroscopic data to constrain the excitation conditions, we obtained gas-phase deuterium abundances [D/H]gas of 0.95+0.54–0.27 x10–5 and 0.87+0.31–0.27x10–5 (statistical errors only) for IC 443C and HH 54, respectively. The uncertainties in the HD abundance are dominated by systematic effects related to the poorly known excitation conditions, and more accurate estimates of the HD abundance in shocked molecular clouds will require measurements of the emission in additional HD rotational transitions.