The role of hydrodynamic instability mechanisms in the presence of laminar boundary layer separation is investigated by means of Direct Numerical Simulations. In a series of simulations involving generic laminar separation bubbles we show that the "natural" onset of unsteadiness (i.e. the development of visible vortex shedding) is not necessarily caused by an absolute/global instability. Our results indicate that the entrainment of high-momentum fluid required to "close" the separation bubble is primarily provided by 2-D or "2-D coherent" structures, which are a consequence of the (inviscid) hydrodynamic instability of the separated shear layer. In a series of highly resolved simulations for a flat-plate boundary layer subjected to low-pressure turbine blade conditions, we demonstrate that this natural instability mechanism (with respect to two-dimensional disturbances) can be exploited for effective control of separation using pulsed vortex generator jets.