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We present the modeling and simulation of 3-D face-centered cubic photonic crystal (PhC) cavities with various defects. We use the plane-wave expansion method to map the allowed modes and photonic bandgaps. Having determined the photonic bands we design specific defects and input-output waveguides and model the coupling between defects and waveguides using the 3-D finite-difference time-domain method. We have calculated the Q-factors and modal volumes (Veff) of the resonant cavity modes for the PhC structures made of materials including germanium (Ge), silicon (Si), gallium phosphide (GaP), titanium dioxide (TiO2), and silica (SiO2). We then use our estimates of Q and Veff to quantify the enhancement of spontaneous emission and possibility of achieving strong coupling with color centers and quantum dots.