Thanks to this thread and a little creativity I've just finished building my new monster (8U) of a server. Thought I would share it with you all to stir up some more creativity:
Basically its 2 of the Xeon servers bolted together. Cut a hole through one, rebuilt the motherboard tray. Added a Norco fan wall and a new Norco back + a second Norco fan wall as the top back. I predrilled and countersunk screw holes for a third Norco fan wall should I find that I want extra cooling later. With the physical size of the case heat buildup is a far, far smaller concern than it would be with a single 4U box.
Case: 2x 4U AIC RSC-4ED2 (modded heavily)
Motherboard: Supermicro X7DBE-X
Processor: 2x Intel Quad Core E5430
RAM: 16 GB DDR2 Memory (original memory from the 2 servers, have a set of 32 GB coming)
Hard Drive: 320 GB SATA OS Drive
Hard Drive Trays: 4 SATA drives for testing (have 14ish more to add soon)
PSU: PC Power & Cooling 750W (since I'm building for lots of extra space I went with low cost PSU, and made it easy to swap out if I find I'm running it hard)
Controller Cards: 6x SUPERMICRO AOC-SAT2-MV8 (48 bays!!!)
OS: Windows Server 2012 + Hyper-V
Taking the server apart and hacking, drilling, countersinking, rebuilding etc. took about a week and a bit of part time effort. Its quite quiet now but I would consider replacing the CPU heatsink fans if I was going to have this thing sitting inside my office all day (they are the quietest of all the original fans but still louder than my desktop). Fortunately it'll be going in a server rack and won't really bother me at all.
For anyone looking for screws for the HDD trays, you can easily scrounge them from the parts you strip off. For instance each original PSU has 12 coarse thread counter sunk screws. Couple more from the case and your sitting quite nicely.