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?
Minzel - Minzel is a beautiful and free mindmapping tool built for creatives and gives you the power to...
Inkscape - Inkscape is a free, open source professional vector graphics editor for Windows, Mac OS X and Linux.
TiddlyMap - An interactive concept- and mind-mapping plugin for the personal note-taking software TiddlyWiki based on the Vis.js library. It's free and open-source!
PGF and TikZ - PGF/TikZ is a tandem of languages for producing vector graphics from a geometric/algebraic...
Mindmaps.app - Mindmaps.app is a browser-based mind mapping software that you can use to generate well-ordered mind maps.
LaTeXDraw - LaTeXDraw is a graphical drawing editor for LaTeX.