Pressure and shear-driven flows of a confined film of fluid overlying a periodic one-dimensional topography of arbitrary shape are considered for prediction of the effective hydraulic permeability in the Stokes flow regime. The other surface confining the fluid may be a planar no-slip wall, an identically patterned wall, a free surface or a surface with prescribed shear. Analytical predictions are obtained using spectral analysis and the domain perturbation method under the assumption of small pattern size to pitch ratio. Using a novel decomposition of the channel height effects into exponentially and algebraically decaying components, a simple surface-metrology-dependent relationship which connects the eigenvalues of the effective permeability tensor is obtained. Two representative topographies are assessed numerically: the infinitely differentiable topography of a phase-modulated sinusoid which has multiple local extrema and zero crossings and the non-differentiable triangular-wave topography. Non-differentiability in the form of corners of triangular patterns and the cusps of scalloped patterns are not found to be an impediment to meaningful and numerically accurate asymptotic predictions of effective permeability and effective slip, contradicting an earlier suggestion from the literature. Several distinct applications of the theory to the friction-reduction and shear-stability performance of the recently developed lubricant impregnated patterned surfaces as well as to scalloped and trapezoidal drag-reduction riblets are discussed, with comparison to experimental data from the literature for the last application. Analytical approximations which have an extended domain of numerical accuracy are also proposed.