FlowMapp - FlowMapp is a UX planning tool for creating visual sitemaps and user flow.
Dia - Dia is a GTK+ based diagram creation program for GNU/Linux, MacOS X, Unix, and Windows, and is released under the GPL license.
Octopus.do - Build your website structure in real-time and rapidly share it to collaborate with your team or clients. Start prototyping websites or apps instantly.
draw.io - Online diagramming application
DYNO Mapper - Create Sitemaps with the DYNO Mapper Visual Sitemap Generator.
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.