I second using a site like pcpartspicker. It can help you avoid some petty technical mistakes, like buying an under capacity CPU cooler, or a power supply without enough of the correct connectors and voltages for your cards.
One thing I've noticed about homebuilt rigs is that they are occasionally louder than normal. I think a lot of builders don't think about noise or airflow, and a lot of the cabinetmakers just provide a bunch of fan mounting points but they can't really consider the cooling needs of the particular motherboard and CPU you're dealing with. If noise is important (perhaps you're going to use it as a media PC in a home theater, too) then you can factor that in as well, or consider options like liquid cooling solutions.