Source: http://feeds.gawker.com/~r/lifehacker/full/~3/313204283/dia-does-powerful-diagrams-and-flowcharts
Windows/Linux only: Open-source application Dia is a robust flowchart and diagram tool. Like a free version of Microsoft Visio, Dia provides you with all the tools you need to create anything from a simple flowchart to a powerful and complex diagram, and files can be saved in many formats, including a Visio Drawing-compatible VDX filetype. Dia is free, Windows and Linux only. If you'd prefer building your diagrams on the web, check out previously mentioned Gliffy.