i love sound paper as a note taking app. IT lets you record while you type, and plays back the audio when you tap on a word. What plays back is what your teacher was saying when you wrote that word. its awesome. But i also use evernote often so i have my notes on my phone, ipad, and computer.
air display is gonna be awesome for writing papers. There as been tons of times i have had to copy a quote down or paraphrase an article and have been switching between them to get the quotes right. i cant wait to use this and put the article on my ipad and type away on my computer.
pages is a good way to read over and make some corrections to your paper. i started half a paper on it and it worked well, just isnt as rounded out as it needs to be to be your go to application for papers.
Your teachers give alot of of pdfs, used to be ibooks wouldnt let you read them and you had to download apps for it. i spent like $20 bucks on these apps cause they all sucked, but to manipulate them iAnnoate PDF and take notes where my 2 favorites. Great to take notes on slides they give out.
Definetely download dropbox. Unless you like paying $100 from apple a year for the same functionality, its basically iDisk with 2gbs free and 20gb for i think $20. But i have never gone over the 2 gb. This is really important for when you forget a file at home you really need, you will still have access to it as long as you have internet.
Wolfram alpha. Its an awesome app and will be an excellent tutor.
so through trial and error thats my top college apps. however, i am considering getting rid of my ipad and getting a bike or something useful because this is way too much of an inbetween device. All those things i mentioned i can do on my laptop or phone. Easier on my laptop in most occasions.