I'm currently using a combination of (mainly free) apps to map my company's website to visualise link flow and indentify isolated content that hasn't been correctly linked in.
I start with a site crawl using Xenu's Link Sleuth from which I can export a list of all pages as well as a list of all the links. I import the two lists into Excel where the data gets cleaned and additional information extracted by a macro. The final step is to import the link and page data in Cytoscape which performs the visualisation.
Don't be fooled by the biological focus of Cytoscape, it will work with any data as long as it's broken down into nodes (pages) and edges (links). It incorporates a number of visualisation algorithms, and allows you to filter a selection of nodes which can then be copied to a subnetwork and visualised separately.
It handles our small site of 2k pages and 50k internal links with ease, and I know a geneticist who uses it to map networks of over 7k genes with some 300k interactions.
If you're interested, I can provide a copy of the spreadsheet I use for manipulating the raw Xenu data.