Hi there,

I'm quite old school and favour manually creating it in Visio! I've done this on very large sites, and while it can take days to do, you get the ideal layout, can colour code pages and use different shapes for different page types.

You also get a very deep understanding of the "as is" state of the site you're interested in.

Check this question out-> Currently, what’s the smoothest site map tool out there? :)

Personally, I prefer FreeMind because it's open source and it's file format is widely used. However, people I present my work to prefer to see it on MS Visio.

Also check out Balsamiq Mockups. It works for site mapping too. You'll just have to exert effort in drawing the arrows there.

I recently used an app called PowerMapper. The UI is fairly grim and it's clear that there has been no UX work on it, but the output can be made to be useful.

Alternatively, the latest version of Visio (2010) in beta also support site mapping.

I am currently using Open Office Draw to create my IA site map.

I am currently experimenting with Prezi as a way of non-linearly documenting site maps. It is the concept of the infinite canvas, and while the tool may not have been intended for sitemaps, I think the concept is interesting. http://prezi.com/

I have to agree with Alex, although as a company we use a variety of different tools including Visio and PowerMapper I personally prefer using Illustrator much more.

yEd Graph Editor is good since people in our team use a number of different operating systems and yEd is cross platform (Java). It's also free and pretty easy to use.

Axure RP Pro for me. By wireframing each page in the site and doing so in a tree view you can automatically generate the site map from it. Also I believe that you can create a prototype app from it to view in a browser, and selecting a node in the sitemap it'll take you directly to view the coresponding wireframe.