Yes I definitely recommend either the Smart Keyboard or the Logitech Create case for your notes and typing. If you will be doing anything hand-written or if you like to draw then absolutely the Pencil. If you get the Smart Keyboard then I'd also recommend a back for it as well.
As for apps, the cool thing is Microsoft office comes free with the iPad but Pages, Numbers, and Keynote are just as good. Spark is great for email. Netflix obviously for study breaks. Hearthstone is also great for relaxing with a fun and good looking game.
Lastly, as macuser82 said, if you can give a bit more info about you'll be using the iPad and what for, we could give some better recommendations. Enjoy the iPad and good luck in school!