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I find IPE to be a life-savior when it comes to generating physics illustrations which come with their share of math toppings. The editor has nice utilities for latching on to the boundaries, intersection, center etc of geometric figures. The spline tool is the best I have seen anywhere. Layers are handled with grace. LaTeX is rendered instantly. It is very easy to produce a multipage document. What more can one possibly want?
Inkscape - Inkscape is a free, open source professional vector graphics editor for Windows, Mac OS X and Linux.
LaTeXDraw - LaTeXDraw is a graphical drawing editor for LaTeX.
PGF and TikZ - PGF/TikZ is a tandem of languages for producing vector graphics from a geometric/algebraic...
Graphviz - Graphviz is open source graph visualization software. It has several main graph layout programs.
TikZiT - TikZiT is a graphical tool for rapidly creating graphs and string diagrams using PGF/TikZ.
Visio - Simplify and communicate complex information using data-linked diagrams.