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
CharacteristicClasses -- Computes CSM classes, Segre classes and the Euler Char. for some Subschemes of Smooth Complete Toric Varieties
CodepthThree -- Classification of codepth 3 local rings based on multiplication in homology
EdgeIdeals -- a package for edge ideals.
GraphicalModels -- A package for discrete and Gaussian graphical models
HighestWeights -- decompose free resolutions and graded modules with a semisimple Lie group action
HodgeIntegrals -- Hodge integrals on the moduli space of curves
InvariantRing -- a package to construct the invariant ring of a finite group
KustinMiller -- Unprojection and the Kustin-Miller complex construction
ModuleDeformations -- Computing versal deformations of maximal Cohen-Macaulay modules
MonomialAlgebras -- Monomial algebras
MultiplierIdeals -- multiplier ideals, log canonical thresholds, and jumping numbers
Nauty -- Interface to nauty
Normaliz -- a package to use Normaliz in Macaulay 2
NumericalAlgebraicGeometry -- Numerical Algebraic Geometry
PHCpack -- Interface to PHCpack
PieriMaps -- computations of matrices between representations of the general linear group based on the Pieri formulas
Polyhedra -- A package for computations with convex polyhedra
Posets -- Package for processing partially ordered sets (posets)
QuillenSuslin -- QuillenSuslin
SimplicialDecomposability -- various decomposability routines for simplicial complexes
ToricVectorBundles -- A package for computations with vector bundles on toric varieties
VersalDeformations -- A package for calculating versal deformations and local Hilbert schemes