I'm a Junior Engineering major and I just recently sold my 12" Powerbook I had for the last two years. I have been wrestling with the same thing and have just about come to the conclusion that an iMac is a better option for me.
Pros for Laptop
Portable so you can take it to class, the library, use in groups, and home on breaks.
Cons for Laptop
Weight - It may only be 5 pounds but when you add it to two textbooks, all of the sudden your bag becomes very heavy. If you are living on campus then you may only need a book or two with you but if you ever plan on living off campus then you probably want to keep a few books with you because hiking to your car at large Universities is a pain.
Fragile - If you drop it or put it between books your investment will be gone. Also, I am very anal so even the smallest scratch makes me upset.
Power/Performance/Price - Lets face it, laptops are less powerful and cost more for an equivalently specced desktop machine.
Rev A bugs-one major current concern for me is that the Rev A bugs haven't been worked out on the MB/MBP machines. Just go read all of the horror stories on this board. Even if I wanted a laptop I would be hesitant after reading them and would consider going with a PC instead because software problems in general are easier to fix than hardware IMO.
Pros for Desktop
Not as Fragile- I guess you could have a freak accident and knock your desktop off of your desk but what are the odds? Also, the internal volume and operation specs aren't as tight so hard drives; logic boards etc. don't fail as often.
Power/Performance/Price - Desktops give you faster, bigger and better specs for less money. The larger/faster hard drives are a big bonus for desktops. Also, the inclusion of GPUs means that you have to go up to a MBP to get similar performance in a lappy for games. (During the holidays of course).
Screen Real Estate - If you are a design major like me (engineering) then screen real estate suddenly becomes very important for projects where you really won't want to spend all of your hours up at the lab working on.
No Rev A Bugs - In general, the iMacs have been pretty problem free. They were just updated to Rev B and I haven't heard any problems yet. This seems to be a solid computer.
Cons for Desktop
Not Portable - There are times when I used my laptop for portability but they were very rare because there are labs everywhere at my university and although there is also Wifi everywhere at my university, it is only a temptation to play a game or check out this board instead of doing what I am supposed to be doing. STUDY! So basically, the lack of portability could be a positive to me because it keeps me off of the computer except for doing work during the day.
So it seems to me that laptops are over-rated because they are distractions in the library when you are studying (sure you can look things up easier, but you can play games/surf easier too) and can't be used as well for gaming machines during breaks when you have time to have fun. Finally, I don't like to be weighed down during the day with stuff I don't really need. I can go into a computer lab any time I need to get on a computer so why do I need a laptop? I guess to look cool... That’s just my perspective but you will have to make up your own mind. Good luck!
EDIT: AS TBi pointed out, another Pro for desktops are the ability to use them as a TV/DVD Player if you live in a dorm room.