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The NFB states in its complaint that this problem isn't unique to Penn State, and having been at several universities myself over the past few years I can certainly confirm that. If the NFB is successful in its complaint (even in part), it will be interesting to see what changes occur at universities. There are a number of legitimately difficult problems to solve to make university web pages accessible -- first, they have a ton of legacy content that would be incredibly costly to fix up if it wasn't created correctly in the first place. Secondly, universities often use complicated (and universally reviled) third-party software packages to which they are all but locked-in -- the NFB lists ANGEL at Penn State; at the University of Rochester we use Blackboard (which was recently certified by the NFB - we joke it is now equally horrible for everyone); at UW they used an in-house project (that was actually accessible, and decently usable). Finally, there is not currently one (or even several) central authorities for university web pages -- at a minimum, each department and organization in the university has its own web presence. These are managed by companies, contractors, in-house people, and students, and so it's not always clear who to blame. Course homepages are even worse as many of these are created by the faculty themselves!
Increasingly, we're seeing people with disabilities resort to legal challenges to accessibility problems - I think this is a natural response to the dismal job we've all done in giving our best effort to create accessible web content. Universities are an interesting case because of the distributed nature of web production, and so it will be especially interesting to see the outcome of this case and what universities do in response.