PAFF - Package for Algebraic Function Fields in one variable. Based on Axiom. Source code is available. - http://www-rocq.inria.fr/codes/Gaetan.Hache/PAFF.html
The algcurves Package in Maple - Examples, test files, plots, documentation. - http://www.math.fsu.edu/~hoeij/compalg/algcurves.html
IntBasis - Algorithms coded in Maple for computing with algebraic curves. The main algorithm computes an integral basis of an algebraic function field using Puiseux expansions. - http://www.math.fsu.edu/~hoeij/compalg/IntBasis/
Ganith - Algebraic geometry tookit for the computation and visualization of algebraic equations. FTP download. - http://www.ticam.utexas.edu/CCV/projects/shastra/toolkits/ganith.html
TESS - C code which computes the Hodge number of complete intersection Calabi-Yau manifolds embedded in products of ordinary projective spaces. - http://www.th.physik.uni-bonn.de/th/People/netah/cy/codes/tess.html
Computing with the Jacobian of a Genus 2 Curve - Pari/GP and Mathematica code to: Compute an equation for a genus 2 curve with a given Jacobian; Move points between the analytic Jacobian (as a torus) and the algebraic Jacobian (as a variety); Work with a fundamental domain for 2 dimensional Siegel upper - http://www.math.lsu.edu/~wamelen/genus2.html
surf - A tool to visualize real algebraic geometry: plane algebraic curves, algebraic surfaces and hyperplane sections of surfaces. - http://surf.sourceforge.net/
INSTANTON - Mathematica program which calculates instanton numbers and other data for Calabi-Yau complete intersections in toric varieties by A. Klemm. - http://www.th.physik.uni-bonn.de/th/People/netah/cy/codes/inst.m
CASA 2.3 - Computer Algebra Software for constructive Algebraic geometry. Designed for performing computations and reasoning about geometric objects in classical algebraic geometry, in particular affine and projective algebraic geometry over an algebraically clos - http://www.risc.uni-linz.ac.at/software/casa/