Anatomy 204 has daily handouts, and occasionally a video and slide shows and text books.
As of this momment that would almost be best done through a centeral website geared for Mobile Safari and a combination of iTunesU. Not only could a website have embedded video material but also interactive demos (talk about a boon to HTML5 adoptors).
How would the university use iTunes vs just picking things off a website?
iTunes through iTunesU will likely be the distribution hub for video and audio lectures. Also depending on the Apps used some that are on the iPod/iPhone right now can download files off the web and into their memory with the right URL header. I use Aji Annotate as my PDF reader and using PDF://someurl.com/thisfile.PDF it will download and save the file. If iWorks and othe programs have such a web interface and acess to thier own file structure you could still use a mostly web interface.
How would students take notes?
I can see where a Microsoft OneNote like program would be great on an iPad.
The hand recgonition program? Well Apple does have in the MacOS but I don't think it has been added to the iPhone. However if finger drawing isn't going to work for you the try a Pogo (I think) iPod/iPad stylus. I hear they are quite good. There is the keyboard doc for faster typing, also Pages or Keynote (depending on amount of graphics) should be a fairly good note taking spaces.
Depends on what document sharing the iPad OS allows, and depends on the App. Some Apps can create an a temportay web server that allows acess to it's files and upload through the web. Well see how robust this gets in a few weeks.
Now this is a hard one, and one i've give a great deal of thought to as a K-8 educator. The first is a Web based test that keeps a single session, if that session I lost (the testie navagates away or closes Safari) the test ends. Not the best answer. Smilar solution, different angle, create a University wide Testing App that logs a student in. This would avoid connectivity drops from send false positves that the student had exited. Again if the student leaves the App during testing the test is terminated.
Other issues include shutting down the iPod/Music App. If you have headphones you can use the clicker to restart a paused playlist. A no headphones policy should be enough but it's better to just write the app in such a way that it won't let the interal music player startup. I don't know of a university that let's students really take tests on an uncontroled computing environment. At K-8, without better parental controls on 3rd Party apps I'd have to reimage the each time and leave just the testing App.