I'm snowed in and analyzing an existing site for a client so we can give the content an overhaul and come up with a content management strategy to minimize maintenance overhead. This is a tedious process that involves clicking links to see where they go, and making notes. It's also a job best done by one person since part of the goal is to recognize areas of content commonality and especially potential commonality.
I started by using SEO Xray to export internal and external links to the lo-tech Excel ss i use to capture my analysis; while this isn't exhaustive (doesn't give a clue about links to files and applications for example) it's a start, and lets me assess the anchor text while I'm at it. I cleared my History first so I can see what pages I've visited and I'm doing the click/review/write tango, using two monitors to maintain my tenuous grip on sanity. I'm also using Google Webmaster Tools link: function to generate input for a start on a context diagram to assess the impact of changes to my site; I'll manually add systems, data sources and libraries that the link: tool doesn't see. And then I'll reconcile the content audit and context diagrams with the site map I generated in Visio.
The first pass through the site is quick-and-dirty to get the lay of the land. Later I'll do a deeper dive, and then cross-ref and collate the audit spreadsheet for areas of commonality, and then look again trying to spot gaps; the stuff that isn't there can be as important as what is when you're migrating and upgrading content...I suggest accompanying all this with a really strong pot of the devil's brew.