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BraidLink
Braidlink is software for knot and braid theory computations. It performs both analytic and numerical manipulations of knots and braids.
http://www.knot-theory.org/
Geomview
Interactive 3D viewing program for Unix. Free under GPL.
http://www.geomview.org/
The Thrackle Problem
John Conway's Thrackle Conjecture: a compilation of what is known about the question.
http://www.thrackle.org/
Topology and Geometry Software
A collection of educational, graphical and research software by Jeff Weeks.
http://www.geometrygames.org/