We present extensive calculations of nonadiabatic couplings (NACs) between the electronically ground and excited states of molecules, using time-dependent density functional theory (TDDFT) within (modified) linear response [C. Hu et al. J. Chem. Phys. 127, 064103 (2007)]. Our approach is implemented in the pseudopotential framework, with the consideration of nonlinear core corrections. The features of either the ordinary Jahn-Teller conical intersections in X(3) (X=Li, Na, K, Cu, Ag, Au) trimers, or the elliptic Jahn-Teller conical intersections in NaH(2), have been well reproduced. In particular, anticipated results for the H-H(2) collision near the avoided crossing are obtained, showing appealing improvement over the first, real-time, TDDFT calculation. The other important type of intersections, Renner-Teller glancing intersection, has also been studied for several typical molecular systems (BH(2), AlH(2), CH(2)(+), SiH(2)(+)), giving results in reasonable agreement with the theoretical model. Despite these successes, it is found that for some systems, including both Jahn-Teller and Renner-Teller systems, the pseudopotential scheme might give inaccurate results for some NAC components on nonhydrogen atoms. By trying different construction schemes of pseudopotentials, e.g., using local pseudopotentials, the results of NACs are found scheme-dependent and show improvement for some cases. Since there is much freedom in constructing ab initio nonlocal pseudopotentials, our findings on TDDFT calculation of NACs in the pseudopotential scheme might be helpful to give clues for constructing more "realistic" pseudopotentials.