I know there are some programs who can be purchased, but I think in your case you might get on best with some of the browser plugins. This way some of the machine-testable stuff you can do by visiting your internal pages with the plugin-infested browser.
Steve Faulkner just came out with some kind of validator called aViewer: http://blog.paciellogroup.com/2013/03/aviewer-2013/ You can actually see the information the browser is passing on to AT with it. It's probably very good for browser builders or to see why something you've built is not being read out as expected by your AT that you're testing in.
I still use the old JuicyStudio Web Accessibility Toolbar (for Firefox and I think maybe other browses too; I get it from addons.mozilla.org). It has a colour contrast analyser and can check for ARIA roles and landmarks (but not if they are correct or anything).
You can check regular HTML (stuff like required alt attributes and document outlines) in the w3c or whatwg validators by pasting HTML presented to your browsers as well (this isn't handy if you've got many many pages, or if some pages only appear after a user has done something).
I'll retwot this post and see if people have more... I don't use many of these tools so I'm out of the loop regarding what's out there... also if someone knows another route you can take besides browser plugins.
*edit someone twotted Fire Eyes from Deque systems.