I reckon build quality, and like Nis said, airflow.
Yup, I'm no master but.
General advice for buying/building a new system:
1. Determine what the system will be used for, and a budget.
2. Research as much as you can about all the parts you intend to buy, and alternatives if the shop doesn't have the item in stock.
3. Try to stick to your budget.
4. Research.
5. If it's your first time building, read the manuals and look at youtube tutorials, and don't force anything in. Pretty much everything's been designed to go in one way, and if you're forcing it in then you're doing it wrong. If you're still not sure, pay the shop or find a techy mate to build it for you. Physical damage is not covered by warranty at most shops.
6. Research.
7. If you're going to be buying parts from MSY Clayton, PLEASE LINE UP IN THE CORRECT LINE.
I built myself a system for about 1350-1400 odd (staff prices and excluding monitor) a few months ago, before the price hikes. I had a general idea of what I wanted to get but now, thinking back, it was such a waste of money.
Intel E8500 (probably the best decision I made while building this system)
ASUS P5Q-Pro (probably not that great a choice for crossfire, being P45 chipset and all)
4gb Kingston HyperX DDR2 800 kit
WD 160gb + WD 640gb
2x 512mb ASUS HD4850s (getting two was waste of money, I don't game often anymore so one card would have been enough)
Antec Nine Hundred case (ricey case ftl, should have waited and bought an Antec P182)
Antec TruePower 650W (good unit, but I wish I got the NeoPower for the modular cables)
The case and PSU were impulse buys, without proper research. Bought the case because what I wanted wasn't available, and I needed a case then and there. The PSU was because CPL didn't have the Corsair HX620s in stock
Oh, advice #8: Don't be impulsive and agree to what the salesman says unless you've researched it beforehand.