In this work we examine the basis functions for those classical and quantum mechanical systems in two dimensions which admit separation of variables in at least two coordinate systems. We do this for the corresponding systems defined in Euclidean space and on the two-dimensional sphere. We present all of these cases from a unified point of view. In particular, all of the special functions that arise via variable separation have their essential features expressed in terms of their zeros. The principal new results are the details of the polynomial bases for each of the nonsubgroup bases, not just the subgroup Cartesian and polar coordinate cases, and the details of the structure of the quadratic algebras. We also study the polynomial eigenfunctions in elliptic coordinates of the n-dimensional isotropic quantum oscillator.