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).
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.
Allowing for redundancy (RAID 5 on six disks for data, and mirrored the boot drives), we ended up with 6.5TB of storage at about $3500 (that includes i7 proc and 12Gb RAM, and a fancy controller). My labor added some more on top of the $3500.
Mostly, we've been happy. It is more sensitive to heat issues than our HP G5s, and of course, generates more of that heat. If I were to go with any kind of density, I'd need a much more robust cooling solution.