Most of the money went to the hard drives themselves. They've come down a lot since (1.5TB had just been announced), but it was around 70% of the cost. Everything else was relatively cheap.
The 2.5 drives are good, and seem to becoming typical, because they run much cooler. We've got some G5s in the same closet, with just as many drives, and they don't run nearly as warm.
Wrt cooling, for actual servers (i.e. not storage nodes) we've had good success with Sun XFires, the 4100+ range. They are very well built and the markup over the SuperMicro junk is minimal (around 15% last time I checked). Among the niceties is a nice array of hot-swap fans - something that SuperMicro still doesn't seem to deliver in their popular chassis.
I'd also consider the xfires for storage nodes if they'd take 3,5" drives, but afaik all their low-end models only have max eight 2,5" slots. That's just no worthwhile density when compared to the larger SuperMicro tins (which go up to 30x3,5" now I think).