You need to factor in drive price vs total price of the system. As an example:
16x 400gb drives give you 6.4TB space (assuming raid 6 you get 5.6TB)
12x 500gb drives give you 6.0TB space, 5.0TB in raid 5.
You can fit 12 drives into quite a few cases, a TJ-07 will do it comfortably with a few 2x5.25" to 3x3.5" converters, and you still get 3x spare 5.25" bays.
In fact that is the setup I have, I have 2x Adaptec 6 channel SATA PCI-X cards from HP Servers. One has 6x 250gb drives on it in the bottom 6 hdd bays in my TJ-07, the other has 6x 320gb drives on it in the cd bays using Lian Li EX23 drive bay converters. I still have 3 cd bays free. What I've done with them is have a DVD-RW drive, a removable SATA rack, and another 2x 5.25" to 3x3.5" rack right up top, using the top cd bay, and the exmpty space at the top of the case. (kind of like having 8x 5.25" bays).
I would suggest a setup like this with a single Areca 12 channel PCIe raid card and any enthusiast level motherboard with 2x PCIe slots like an Asus P5W DH, P5N32-E, A8N-SLI, whatever. 12x 500gb drives in a setup like this will cost you a lot less than 16x 400gb drives because with 16 drives you will need to go up to the next level of case size, controller card, and you will have even more case and cooling problems
I use an Acbel 550w psu to power the motherboard, cpu (p4 3.46ghz ee) and 4 of the drives at the bottom of the case, and an Enermax 701AX to power the remaining drives.