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asciiflow - Infinite ASCII diagrams, save to Google Drive, resize, freeform draw, and export straight to text/html.
PGF and TikZ - PGF/TikZ is a tandem of languages for producing vector graphics from a geometric/algebraic...
Core2D - A multi-platform data driven 2D diagram editor.
Inkscape - Inkscape is a free, open source professional vector graphics editor for Windows, Mac OS X and Linux.
PathVisio - Open-source and free pathway analysis and pathway drawing software. Allows drawing, editing and analysis of biological pathways.
Graphviz - Graphviz is open source graph visualization software. It has several main graph layout programs.