Nauty  
   A program for computing automorphism groups of graphs and digraphs. It can also produce a canonical labelling.
   http://cs.anu.edu.au/~bdm/nauty/

Free Software in Graph Theory  
   Free Software for Win 9X,NT on Graph Theory by Vitali Petchenkine. Procedures: Metrics of the graph; Paths and cycles; Colorations; Automorphism group; Minimal spanning tree; Shortest paths; Max. Capacity pat
   http://www.geocities.com/pechv_ru/

Scalable Libraries for Graph Partitioning  
   We are pursuing research in the area of new parallel methods for graph partitioning and incremental graph partitioning. Efficient methods for graph partitioning and incremental graph partitioning are important for parallelization of a large nu
   http://www.npac.syr.edu/NPAC1/PUB/ranka/part/part.html

Gato: The Graph Animation Toolbox  
   Software for visualizing graph algorithms. Free under GPL. Unix, Linux, MacOs ad Windows versions.
   http://www.zpr.uni-koeln.de/~gato

plantri and fullgen  
   Programs for generation of certain types of planar graph, generated in such a way that exactly one member of each isomorphism class is output without the need for storing them.
   http://cs.anu.edu.au/people/bdm/plantri/

Algorithms and Software for Partitioning Meshes  
   Using combinatorics to solve structured linear systems of equations.
   http://www.cs.sandia.gov/CRF/chac.html

METIS: Family of Multilevel Partitioning Algorithms  
   Graph, mesh, and hypergraph partitioning software.
   http://www-users.cs.umn.edu/~karypis/metis/

SF, Posets and Coxeter/Weyl  
   John Stembridge's Maple packages for symmetric functions, posets, root systems, and finite Coxeter groups.
   http://www.math.lsa.umich.edu/~jrs/maple.html

Combinatorics Software of the Algorithms Project  
   Combinatorial analysis, discrete mathematics and computer algebra are the main interests of the Algorithms Projects. The packages let you define combinatorial structures; manipulate the associated generating functions, functional equations or recurrences;
   http://algo.inria.fr/libraries/software.html

GraphThing  
   Tool for investigating Graph Theory, with a GTK interface. Free under GPL. Unix, source code in C++.
   http://graph.seul.org/

LINK: A Software System for Discrete Mathematics  
   A general-purpose, extendible computing environment in which discrete mathematical objects representing real world problems can be easily manipulated and visualized.
   http://dimacs.rutgers.edu/~berryj/LINK.html

Graph Coloring By DSATUR  
   By using the DSATUR algorithm, this php/form colors any graph in the Dimacs format.
   http://prolland.free.fr/works/research/dsatphp/dsat.html

JGraphT  
   Free Java class library that provides mathematical graph-theory objects and algorithms.
   http://jgrapht.sourceforge.net

GeoSteiner  
   Software for computing Steiner trees. Written in ANSI C, includes the public domain LP-solver lp_solve.
   http://www.diku.dk/geosteiner/

Information System on Graph Class Inclusions  
   A java applet for researching what is known about particular graph classes.
   http://wwwteo.informatik.uni-rostock.de/isgci/

GRAPE  
   A GAP package for computing with graphs; primarily designed for the efficient construction and analysis of graphs related to groups, combinatorial designs and finite geometries.
   http://www.maths.qmul.ac.uk/~leonard/grape/

GOBLIN Graph Library  
   C++ library of graph optimization algorithms with a GUI for editing, running and tracing the algorithms.
   http://www.math.uni-augsburg.de/opt/goblin.html

ACE  
   An Algebraic Combinatorics Environment for MAPLE providing functions to work with classical structures in algebraic combinatorics. Free download.
   http://phalanstere.univ-mlv.fr/~ace/ACE/3.0/ACE.html

Graph Partitioners  
   Three algorithms written in NESL for finding separators of graphs, in order to compare the quality of the cuts.
   http://www-2.cs.cmu.edu/~scandal/alg/separator.html

Project Vega  
   A system for manipulating discrete mathematical structures: a Mathematica based collection of operations with interface to external packages and programs.
   http://vega.ijp.si/Htmldoc/Vega03.html