In particular, I'm looking for a tool (web or desktop / free or paid) that can spider an entire site and check Section 508 compliance. (WCAG 1 and 2 would be a nice bonus too)
There are plenty of tools (including the Web Developer Toolbar for firefox) that can check
But that's not what I'm looking for. I'm looking for something that can check an ENTIRE site and generate a report. Price is not much of a factor.
Seems like if you're using some sort of CMS, checking one page at a time doesn't wouldn't be that big of a deal. You're working with templates, file includes and one or more dynamic menu generators, and one set of changes to accessability - alt tags, capability to tab through menus, or even a "shadow" site of plain text 508-compliant pages, etc. - will cover much of the work. Many CMSs are fairly compliant to begin with.
That said, there's a review of commercial checking software here.