We describe two different implementations of time-dependent density functional theory (TDDFT) for use in excited state molecular dynamics simulations. One is based on the linear response formulation (LR-TDDFT), whereas the other uses a time propagation scheme for the electronic wave functions (P-TDDFT). Photo-induced cis-trans isomerization of C=C, C=N and N=N double bonds is investigated in three model compounds, namely the 2,4-pentadiene-1-iminium cation (PSB), formaldimine and diimide. For formaldimine and diimide, the results obtained with both schemes are in agreement with experimental data and previously reported theoretical results. Molecular dynamics simulations yield new insights into the relaxation pathways in the excited state. For PSB, which is a model system for the retinal protonated Schiff base involved in the Visual process, the forces computed from the LR-TDDFT S-1 surface lead to an increased bond length alternation and, consequently, to single bond rotation. On the contrary, P-TDDFT dynamics lead to a decreased bond length alternation, in agreement with CASPT2 and restricted open-shell Kohn-Sham (ROKS) calculations.