Pulsed lasers offer significant advantages over continuous wave (CW) lasers in the coherent control of qubits. Here we review the theoretical and experimental aspects of controlling the internal and external states of individual trapped atoms with pulse trains. Two distinct regimes of laser intensity are identified. When the pulses are sufficiently weak that the Rabi frequency X is much smaller than the trap frequency omega(trap), sideband transitions can be addressed and atom-atom entanglement can be accomplished in much the same way as with CW lasers. By contrast, if the pulses are very strong Omega >> omega(trap), impulsive spin-dependent kicks can be combined to create entangling gates which are much faster than a trap period. These fast entangling gates should work outside of the Lamb-Dicke regime and be insensitive to thermal atomic motion.