The <a href="http://en.wikipedia.org/wiki/Mukai-Fourier_transform">Fourier-Mukai transform</a> comes from a bimodule: the Poincaré bundle. Let $A$ be an abelian variety, the Poincaré bundle $\mathcal{P}$ is a vector bundle on $A \times \hat{A}$ coming from the fact that the points in the dual abelian variety $\hat{A}$ parametrize line bundles on $A$ ($\mathcal{P}$ is the universal family). In the Fourier-Mukai construction, $\mathcal{P}$ is used as a $\mathcal{O}_A$-$\mathcal{O}_{\hat{A}}$-bimodule to produce a functor between the derived categories of coherent sheaves on $A$ and $\hat{A}$ via a push-pull construction.