Comment Note Taker HD (Score 1) 425
I went "paperless" taking two graduate mechanical engineering classes this semester, using Note Taker HD on the iPad. It takes some getting used to, but once you figure out the workflow issues (Good Reader and Drop Box are a must), it is incredibly convenient. I evaluated 8 or 9 different iPad note taker apps, and at the time (August 2011), the only one that could do everything I wanted (easy PDF import for annotations, zoom feature, ability to draw shapes, easy export) was Note Taker HD.
You will also NEED a stylus. Controlling a tablet UI is fine with your fingers - writing text and drawing diagrams for an hour during a class with your fingers just doesn't cut it. I love my Wacom stylus for iPad, though I have actually worn through it in just 3 months. You will probably need to try several (I tried 3 different ones) before you find the one that is right for you.