Here is how I use my iPad at my local state college.
1: Goodreader - This thing has been my salvation for pdfs / textbooks. If you can't get your textbooks in PDF, then there is still always the Nook software, CourseSmart, Inkling (nice books, small collection), etc.
2: Evernote - I use this to read my notes, not write them. I hate the fact that Evernote isn't using real text input. However, for organizing and reading it is a bowl of win. Which leads me to my next part...
3: Pages: While not the best text/word processor, it does allow for writing bullet lists which I take my notes in. After finishing with a chapter's note, I email the completed document in PDF to my Evernote email address which places the note in my Evernote notebook.
4: JotNot Pro (iPhone) - I use this to "scan" documents and forward the compiled PDF to Evernote. This allows me to keep important tests for review on hand if I need it. If I want to make annotations, I've been sending the PDF out of JotNot Pro to Dropbox and then forwarding the it on to Noterize via Goodreader. Afterwards, I take the annotated pdf from Noterize and email it on to Evernote. You don't need to use JotNot Pro if you don't have an iPhone. A scanner works just as well or any of the other "scanner" apps for the iPhone if you have one.
5: Dropbox - Essential..absolutely... This works as a great medium for those documents that you need to move around, but don't feel like syncing your iPad to a computer to get them on there. Just place it in your Dropbox and go.
6:Wolfram Alpha - Really Good Program for figuring out those hard to do math problems or getting a clue on what you are doing wrong. I've used it for Calculus and Trig and never have been steered wrong.
7:Todo by Appigo - Awesome Todo app for the iPad. It has been keeping me on task and organized so that I can get things done.
Major thing is workflow. Found that once you have how you are going to do things, the iPad becomes much more useful for schooling.