My main check so far has been to ensure I comply to the guidelines. In my role I can access screen readers (JAWS, Supernova and Zoom text) and I am also able to consult with students with dyslexia, Asperger syndrome and those who are D/deaf, blind or visually impaired. However these are all busy people and I do not want to impose on their time, so I tend to restrict this form of testing to essentials. I have also had a good response from my PLN on Twitter as three people tested and commented on my resource. This enabled me to check accessibility on other Windows' browsers such as Internet Explorer, Firefox and Opera; and also on Mac OSX 10.6, Firefox and Safari version5.
I am reluctant to totally rely on accessibility tools although I intend to try out one or two to see if they concur with manual methods of assessment.
For a large VLE system I would consider that the most efficient way to test it would be to supply guidelines to everyone adding material to the VLE and then appointing one person per department to assess conformance to these guidelines, either manually or by automated checker. I would also like to see a quick, easy and accessible (!) method to report any problems to a manager so that the student does not have to contact each lecturer individually in order to ensure they can access the material. In this way the student does not have to personally complain to the person who was marking their work and it is shown that senior management take the issue seriously.