The famous Johnson-Nyquist formula relating noise current to conductance has a microscopic generalization relating noise current density to microscopic conductivity, with corollary relations governing noise in the components of the electromagnetic fields. These relations, known collectively in physics as fluctuation-dissipation relations, form the basis of the modern understanding of fluctuation-induced phenomena, a field of burgeoning importance in experimental physics and nanotechnology. In this review, we survey recent progress in computational techniques for modeling fluctuation-induced phenomena, focusing on two cases of particular interest: near-field radiative heat transfer and Casimir forces. In each case we review the basic physics of the phenomenon, discuss semianalytical and numerical algorithms for theoretical analysis, and present recent predictions for novel phenomena in complex material and geometric configurations.