What tool (Windows or Mac) do you like for making web sitemaps (something along the lines of this – without the colours) http://www.avermedia.com/AVerTV/Upload/SpecialPagePic/sitemap.gif)
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You could give the free diagramming tool “yEd” a try, which happens to work on both Windows and Mac (as well as Linux, because of its Java based nature).
Start off with the tree structure of your diagram (the page hierarchy) and let the tool automatically layout that part for you. Then add the links that between the pages that are “cross-references” and don’t follow the hierarchic structure of your website, select them and run an edge routing algorithm (“Orthogonal Edge Router”) on the selected edges. Play with the different layout algorithms and their settings to find a picture that suits your needs.
Finally you can export the graphic into a bitmap, or even an SVG graphic or interactive Flash graphic to include into your website.