The one I like most is the yEd Graph Editor.
It is very easy to use, filled with options, runs on Windows, Unix/Linux, Mac OS X, and FREE.
It supports many graph formats, like:
The SVG export option is awesome for publishing the resulting graph, but it can also export in PNG, JPG, PDF, SWF.
It can automatically import Excel XLS files or XML files and generate the graph.
Also it can import palettes of graph symbols from graphML palette file (.graphML) or Microsoft Visio Stencils (.vdx, .svx), and you can also create your own or search and download other glyphs using the integrated IconFinder option.
The auto grouping and auto layout features are the most complete and easy to use I've found.