LinBox: C++ template library for exact, high-performance linear algebra computation with dense, sparse, and structured matrices over the integers and over finite fields
M4RI: A library for fast arithmetic with dense matrices over GF(2)
matplotlib: Python plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms
Maxima: System for manipulating symbolic and numerical expressions
Mercurial: Free, distributed source control management tool
mpmath: Pure Python library for multiprecision floating-point arithmetic
mwrank: Program for computing Mordell-Weil groups of elliptic curves over Q via 2-descent. Since November 2007 mwrank has formed part of the eclib package
NetworkX: Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks
SageTeX: The SageTeX package allows you to embed code, results of computations, and plots from the Sage mathematics software suite into LaTeX documents
Singular: Computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory
Sphinx: A tool that makes it easy to create intelligent and beautiful documentation
SQLAlchemy: Python SQL toolkit and Object Relational Mapper that gives application developers the full power and flexibility of SQL
SQLite: Software library that implements a self-contained, serverless, zero-configuration, transactional SQL database engine
Symmetrica: Collection of C routines for representation theory
SYMPOW: Package to compute special values of symmetric power elliptic curve L-functions