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?
LucidChart - LucidChart is the missing link in online productivity suites. LucidChart allows users to create, collaborate on, and publish attractive flowcharts and other diagrams from a web browser.
Inkscape - Inkscape is a free, open source professional vector graphics editor for Windows, Mac OS X and Linux.
OmniGraffle - OmniGraffle is for creating precise graphics like website wireframes, an electrical system designs, or mapping out software class.
LaTeXDraw - LaTeXDraw is a graphical drawing editor for LaTeX.
draw.io - Online diagramming application
yEd - yEd is a free desktop application to quickly create, import, edit, and automatically arrange diagrams. It runs on Windows, Mac OS X, and Unix/Linux.