Xeon E6540 's Advantages
Higher specification of memory (1333 vs 3)
Larger L3 cache size (18MB vs 12MB)
Lower TDP (105W vs 130W)
Intel Xeon E5 1650 's Advantages
Released 2 years late
Newer PCIe version (3 vs 2)
Higher base frequency (3.2GHz vs 2GHz)
More modern manufacturing process (32nm vs 45nm)