DYNO Mapper - Create Sitemaps with the DYNO Mapper Visual Sitemap Generator.
UX Flow Wireframe Prototyping System - Create beautiful user flows prototypes for your next project
A1 Sitemap Generator - A1 Sitemap Generator has been in active development and sold since 2005.
draw.io - Online diagramming application
PowerMapper - Create visual HTML site maps and XML sitemaps for search engines of any web site quickly and easily.
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.