You may want to take into consideration the Virtualization support on both processors.
Intel® Xeon Processor X5690 supports Intel® Virtualization Technology (VT-x) and Intel® Virtualization Technology for Directed I/O (VT-d) while the Intel(R) Xeon Processor E7-4807 only supports Intel® Virtualization Technology (VT-x).
Furthermore, the Intel® Xeon Processor X5690 runs at a higher clock speed and supports Intel® Turbo Boost Technology while the Intel(R) Xeon Processor E7-4807 runs at a lower clock speed and does not support Intel® Turbo Boost Technology.
At this point, what will make the difference is which of the processor is the one better meeting your needs according to the software that will be in use; whether Intel® Virtualization Technology for Directed I/O is needed or not, and whether you want a processor with a higher speed capability or not.
Comparison chart can be found here: http://ark.intel.com/compare/53569,52576
Intel® Xeon Processor E7-4807: http://ark.intel.com/products/53569
Intel® Xeon Processor X5690: http://ark.intel.com/products/52576