Well...
If you have nothing at all, and you want to have a machine that's somewhat well-rounded, then a Laptop is a no-brainer. My first 3 years in college, I survived doing my papers, media watching, and countless hours of WoW on my dilapitated Gateway 7426gx.
Now, I upgraded to a Desktop for gaming/main machine. Though (stupidly) I still went for a sub-$1k laptop, where if I waited 3 or so months later I could have found and gotten myself a netbook that would fit all my portable needs without the massive hit on the wallet.
For me, my desktop is a off-the-shelf variety, just because I didn't want the hassle of building it myself, and BB was doing a bitching special on a monitor+tower+printer deal at the time that I just went with it. More often than not, I would buy a basic model from the shelf, and do a number of incremental upgrades overtime, until the unit is no longer recognizable from the shelf models.
I miss building my machines though, and I've been thinking to build a simple sub $500 machine for my fiancee's nephew that moved in with us, so I might go that route.