Surface-enhanced Raman scattering (SERS) spectra contain information on the chemical structure on nanoparticle surfaces through the position and alignment of molecules with the electromagnetic near field. Time-dependent density functional theory (TDDFT) can provide the Raman tensors needed for a detailed interpretation of SERS spectra. Here, the impact of molecular conformations on SERS spectra is considered. TDDFT calculations of the surfactant cetyltrimethylammonium bromide with five conformers produced more accurate unenhanced Raman spectra than a simple all-trans structure. The calculations and measurements also demonstrated a loss of structural information in the CH2/CH3 scissor vibration band at 1450 cm-1 in the SERS spectra. To study lipid bilayers, TDDFT calculations on conformers of methyl phosphorylcholine and cis-5-decene served as models for the symmetric choline stretch in the lipid headgroup and the C═C stretch in the acyl chains of 1,2-oleoyl-glycero-3-phosphocholine. Conformer considerations enabled a measurement of the distribution of double-bond orientations with an order parameter of SC═C = 0.53.