The present paper gives an overview of the recent modelling activities under NATO-STO AVT-349, focused on the understanding and modelling of boundary layers for incompressible, high-Reynolds-number flows subject to non-equilibrium conditions such as strong pressure gradients, three-dimensionality, and surface roughness and heterogeneity. For this, we consider simpler cases where the above flow conditions are present separately or in a reduced number of combinations. First, we focus on the effect of roughness on the outer flow and the problems associated to its characterisation and prediction, with a particular emphasis on the conditions necessary for outer-layer similarity to hold. We then focus on how the presence of adverse and favourable pressure gradients affects the effect of roughness, and to what extent the figures used to quantify it are still useful under such conditions. We also consider the effect of surface heterogeneity, the shortcomings when modelling it and how these can be addressed. We then focus on the effect on the outer layer of pressure gradients and non-equilibrium conditions, to what extent similarity holds in those conditions, and how RANS models perform for such flows, identifying routes for their improvement to handle pressure gradients and non-equilibrium. We also discuss the use of data-driven and machine-aided methods in closure models.