What applications do you use and how ?
Pages - It's really up to you which word processor you want. I use pages and have never really had a problem. There are free alternatives but I can't think of the name of them right now. Google will help you there.
Dropbox - In my opinion this is truly a must have. If you don't already know what it is, it adds a folder to your home folder that syncs with the web. Anything in this folder you can access on the web at dropbox.com. It's extremely helpful because if you forget a file or something it's always available online. It comes with 2GB of storage for free or you can pay for more.
iStudiez - This will help you keep track of courses, grades, GPA, exams, and assignments.
Anxiety - It's a very simplistic todo list application but it gets the job done. I usually use this to make a list of assignments I need to do and then have it open on startup so that way every time I turn on my MacBook, I'm reminded of what I have to do.
SelfControl - This is probably the most useful app I've used and it doesn't seem to be pretty well know. It will save your life if you're trying to study or get things done, but you keep getting distracted by other things on the web such as Facebook. What is does is you input a list of websites that get you distracted when you study (Facebook, Youtube, Twitter, etc.) and you start a timer anywhere from 15 minutes to 24 hours with 15 minute intervals. Once you start the timer, the app prevents you from accessing those websites. No matter what you do (quitting the app, restarting your computer, etc.) you cannot access those websites until the time is up.
VirtualBox/Boot Camp - It's usually inevitable that you'll come across something that requires Windows and these are two free options which allow you to run Windows with your Mac. You will have to obtain a copy of Windows though.
So how's the best way to organize an efficient workspace on your computer ?
I usually use multiple Spaces (Desktops in Lion). I'll have Safari in one Desktop, iTunes in another, Pages in another, etc. With it set up like this it reduces clutter. Don't go overboard though. I've never had more than 4 spaces occupied at one time.
Another good thing to have around is
BetterTouchTool. It lets you add custom multitouch gestures but it also will enable window snapping which allows you to easily set one window to the left side of your screen and a different window to the right side of your screen (I'll post a screenshot). This is extremely useful if you're typing a paper and using Safari for research at the same time.