Whilst not in the same category as Visio I am a huge fan of the wire framing tools provided by Balsamiq. While on the topic of wire framing (which is useful in addition to site map tools like Visio) Smashing Magazine recently had an excellent article on wire framing resource.
I use illustrator to draw basic boxes for very raw webpage layout images. Previously I used Photoshop to build visually complex mockups of websites. Now I skip the photshop stage and go straight to code.
I use a css framework called blueprint (http://www.blueprintcss.org/) to quickly build interfaces. It includes a grid system, css reset, typography and forms, etc.
Sitemaps can be drawn using mind mapping software. I use omni graffle (I work on a mac) It works well.
