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We present new evolution sequences for very low mass stars, brown dwarfs and giant planets and use them to explore a variety of influences on the evolution of these objects. We compare our results with previous work and discuss the causes of the differences and argue for the importance of the surface boundary condition provided by atmosphere models including clouds. The L- to T-type ultracool dwarf transition can be accommodated within the Ackerman & Marley (2001) cloud model by varying the cloud sedimentation parameter. We develop a simple model for the evolution across the L/T transition. By combining the evolution calculation and our atmosphere models, we generate colors and magnitudes of synthetic populations of ultracool dwarfs in the field and in galactic clusters. We focus on near infrared color- magnitude diagrams (CMDs) and on the nature of the ``second parameter'' that is responsible for the scatter of colors along the Teff sequence. Variations in metallicity and cloud parameters, unresolved binaries and possibly a relatively young population all play a role in defining the spread of brown dwarfs along the cooling sequence. We find that the transition from cloudy L dwarfs to cloudless T dwarfs slows down the evolution and causes a pile up of substellar objects in the transition region, in contradiction with previous studies. We apply the same model to the Pleiades brown dwarf sequence. Taken at face value, the Pleiades data suggest that the L/T transition occurs at lower Teff for lower gravity objects. The simulated populations of brown dwarfs also reveal that the phase of deuterium burning produces a distinctive feature in CMDs that should be detectable in ~50-100 Myr old clusters.