First, a top five list - notable for a different flashcard application (I still like Quizlet a lot), another graphing calculator to try, and Evernote which I actually like and use. I'm planning to try the project app soon. Here's the link.
Next, here's a list from Lifehacker for the Mac Student
Continuing our Apple/Mac theme, here are 8 more.
And this' year's updates list from AppStorm here.
Know what doesn't work very well? Those big paper calendars that lie flat on your desk. Seems like it would be handy to write on, easy to see for reminders, etc. The reality? That's where I put stuff down or spread my work out on the desk, covering it up.