jskrewson - I understand what you're saying about buying something off the shelf and the value of your time. I build my own computers and it is an investment.
Just a quick mention since SSDs came up. I don't know your total storage needs, but keep an eye out next year for drives like OCZs Z drives. They make Enterprise class SLC devices (up to 512 gig) as well as MLC devices (up to 2 TB).