The no-slip boundary condition was considered to have been experimentally established for the flow of simple liquids over solid surfaces in the early 20th century. Nonetheless the refinement of a number of measurement techniques has recently led to the observation of nano- and microscale violations of the no-slip boundary condition by simple fluids flowing over non-wetting surfaces. However it is important to distinguish between intrinsic slip, which arises solely from the chemical interaction between the liquid and a homogeneous, atomically flat surface and effective slip, typically measured in macroscopic experiments, which emerges from the interaction of microscopic chemical heterogeneity, roughness and contaminants. Here we consider the role of both intrinsic and effective slip boundary conditions in nanoscale and microscale fluid flows using a theoretical approach, complemented by molecular dynamics simulations, and experimental evidence where available. Firstly, we consider nanoscale flows in small capillaries, including carbon nanotubes, where we have developed and solved a generalised Lucas-Washburn equation that incorporates slip to describe the uptake of droplets. We then consider the general problem of relating effective slip to microscopic intrinsic slip and roughness, and discuss several cases where we have been able to solve this problem analytically. Finally, we look at applications of these results to carbon nanotube growth, self-cleaning surfaces, catalysis, and putting insulation in your roof.