Honestly I would say it depends on your school's facilities. Do they have wireless internet in most locations? Are there easily-accesable computer labs where you can bring a usb drive into? When you give powerpoint presentations, will there already be computers hooked up to projectors, so that all you need is a usb drive with your file on it? For me, at Purdue, this was the situation. Honestly, either choice would be viable. However, as a Junior/almost Senior in college who has used both desktops and laptops, here's what I wish I knew before I arrived as a freshman:
With regards to the combo, I agree with merlin - it's a little wasteful and not very effecient. Either one of the computers will become your "main" over time while the other is neglected, or you will have to constantly sync your files. If you get a desktop, it's perfectly acceptable (and even better often times) to take notes by hand, and it can be easier to draw up charts and graphs on the fly that your professors may throw up on an overhead. If you spend alot of your free time on the computer surfing the net, chatting, etc as I do, wouldn't you want it to be on a big beautiful screen with great specs? Laptops are kind of nice in that you can watch movies in bed with your girlfriend, though, so that's something to consider.
I used to have a small form factor Shuttle PC that I built with a big lcd as my main desktop, I loved it. It was pretty powerful and played every game on the market beautifully. Then I started obsessing over laptops, thinking that I *had to have* that lovely portability. Since I was going to study abroad for a year (still am in Japan at the moment), that was my excuse to sell the desktop to my dad and buy a laptop. Here's my thoughts on laptops in general - if you're going to get one, make sure it's small and portable. I have a 6.3 pound, 1.33" inch thick, 15.4" widescreen Asus laptop. This thing is too big and uncomfortable to carry around campus, and it has a huge footprint. This is especially apparent in class, and during the few occasions when I brought it into the class to "take notes" (aka surf the net during boring lectures) it just felt too big and out of place.
Meanwhile, my friend's 12" powerbook is slim and trim and he carries it everywhere he goes with a protective sleeve in his messenger bag. My next laptop will be no more than an inch thick, and I'm hoping that the Macbooks will meet this requirement more or less when they are released. If not, I might just be stuck getting another PC, like a Sony TX series (13.3" widescreen, extremely thin) and putting linux on it or something. I don't personally like small screens, but the only reason I'm getting another laptop is because I'm planning on more international travel (coming back to Japan again) after graduation. If I wasn't going to be traveling more, I would just buy a Mac Mini with a 20" cinema display and call it quits (I don't like headless computers; but in your case, it would probably be an iMac right?). Hope this helps you out in your decision.