The closest I seen in a quick look, Intel® Server Board S1200KPThe perfect MB for that project doesn't exist...but if it did it would be something like this:
Mini-ITX
Socket LGA1155 (IB Xeons)
C206 or similar chipset to support ECC
4x DIMM sockets for 32GB
2x X540 LAN (you'll want the option of 10G-baseT for access to SAN)
2x mSATA sockets connected to the SATA-III links of the chipset - boot from mSATA
up to 4 SATA-II connectors exposed as space on MB permits (will probably never be used...)
PCIe socket - at least x8 but x16 if space permits
Support for vPRO/AMT for management
Video out from CPU - nothing fancy, RGB will do - DVI or DP OK too.
At least 3 PWM fan headers
USB-3 MB connector
4x USB-3 exposed on rear IO
Support for VT-x & VT-d
Since you want to mount it in 1U the RAM sockets need to align longways front-to-back for airflow/cooling.
You don't need/want any more bells or whistles...given 6-8 of these and a 12-port 10Gbase-T switch like the new Netgear and you could build a heck of a little compute cluster. Small, reasonable power, reasonable cost.
Love the lego cluster.