Here's my opinion. Being as I am in grad school (albeit in chemistry) I can give some advice.
1) Get the best CPU you can afford (with in reason obviously). Meaning don't spend $300 for an additional 100mhz
2) Maximize your ram amount by installing it yourself. Check the prices of ram and see what ends up getting you the best deal. Buying 4GB yourself and getting the bare minimum or buying 2GB single stick and 2GB yourself. Sometimes one is cheaper sometimes the other is cheaper (often times it is the first option suprisingly enough)
3) Same thing with a hard drive. For example, I have seen a 500GB SATA 2.5" HD go for around $100, while as an upgrade it would cost you 200+. There is an EXTRA benefit in this scenario. If you get the $500gb HD yourself, the HD that is in there you can use as a backup drive, just by purchasing a USB enclosure.
4)A graphics card isn't a bad thing to have, especially since you are going into computer programming. THe reason I say this, there are languages designed to allow the cards to act as SMP machines. Just throwing that out there. I just wouldn't make it your top priority.
5) Warranty, warranty types and reliability - These are all parts of the same coin. Honestly, I would look more at buisness lines (i.e. Dell's Buisness line or Lenovo). In college you CAN'T afford for your computer to be down for mutliple days or sent off for warranty repairs. The buisness lines tend to be much more reliable and in the case of Dell, they come with Next Day ON SITE service. This means at most your laptop is down for 48hrs (inclduing diagnosis and the shipping of the part). There is NO sending it out, no waiting for repairs, etc. On top of that GET THE WARRANTY that covers ACCIDENTAL damage. This is a MUST in college. No if ands or buts about it.
As for apples. They are nice machines, but they are mainly status symbols. Also, their reliability is not as great as some would have you believe. Since your are in GeekU, I don't think you will need to worry as much about malware anyways. The upside to a mac, is you will have that platform to program on as well and well they are GORGEOUS machines (some of them).