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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?
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What problems do you have with all the existing options (just a couple links I picked from a google search)? Source: almost 2 years ago
Code2Flow - An easy solution to create product flows.
Inkscape - Inkscape is a free, open source professional vector graphics editor for Windows, Mac OS X and Linux.
DIagrams Through Ascii Art - Java command-line tool to convert ASCII diagrams to bitmaps.
PGF and TikZ - PGF/TikZ is a tandem of languages for producing vector graphics from a geometric/algebraic...
Asciio - Perl application to draw ASCII diagrams in a simple, modern graphical interface.
LaTeXDraw - LaTeXDraw is a graphical drawing editor for LaTeX.