It certainly depends a lot on your major. Look at the web page for the program you're thinking of going into. They may have technology requirements or recommendations that will help you decide.
Generally, architecture and engineering programs require Windows computers.
Advertising and art students are advised to go with Macs.
Computer science students can go with either, although computer engineering students should go with Windows.
I would personally recommend going with a Mac for the sole reason that you can install the Windows operating system on a Mac. Windows 7 is sold at a discounted price for students. Depending on the school you go to, it may be even more heavily discounted. (At my school, I purchased Windows 7 for $17.) So if you buy a Mac, you can, in a way, get a Windows computer as well.
Here's an Apple link about Windows on Mac: http://www.apple.com/macosx/compatibility/
I wouldn't recommend Linux. It's not user friendly, and won't give you many advantages if you're not huge into developing your own applications and modifying your operating system. It's just not worth the hassle.