The first time you build a desktop it will be at least as expensive as a pre-made if not a little more. The big determining factor is going to end up being in software and peripherals.

If you have a .edu student e-mail or have a good friend with such an e-mail address you can save massive amounts of money.
HP runs great deals for students on monitors and printers.
If I remember correctlly it's digital river and you can get Win 7 professional for about $80 and Office 2010 for another $100 or so with the .edu e-mail.

The computer itself will be a wash this time. But here's my expierence. I built my first PC about 3.5 years ago, it cost a little more than most pre-mades. But the features were exactlly what I wanted. Since then I've tinkered and added/upgraded here and there. These expanded features and upgrades have probably saved me the cost of a whole new machine to be where I'm at now.

I got curious about my PC vs. today's i7 pre-mades that you can get at Best Buy etc... I a simple comparison using the windows rating. My system overall is rated at 5.4 (Processor 7.2, RAM 7.2, Gaming graphics 6.6.) Most of the Best Buy machines were sub 4 off the shelf.

Anyways this is just my 2 cents.