Here is a list of the packages that are distributed with Macaulay2. The ones that have been refereed are marked with a star.
Binomials -- Specialized routines for binomial ideals
EdgeIdeals -- a package for edge ideals.
HodgeIntegrals -- Hodge integrals on the moduli space of curves
ModuleDeformations -- Computing versal deformations of maximal Cohen-Macaulay modules
Normaliz -- a package to use Normaliz in Macaulay 2
NumericalAlgebraicGeometry -- Numerical Algebraic Geometry
PieriMaps -- computations of matrices between representations of the general linear group based on the Pieri formulas
Polyhedra -- A package for computations with convex polyhedra
SimplicialDecomposability -- various decomposability routines for simplicial complexes
ToricVectorBundles -- A package for computations with vector bundles on toric varieties