However, analysts agreed that beyond the number of cores, factors such as on-chip cache, RAM and memory bandwidth help improve system performance. Intel is putting four memory channels in the Nehalem-EX chips, which puts it on par with AMD's Magny-Cours chip.

For most enterprise applications, memory throughput is a significant contributor to performance, McCarron said. For example, memory bandwidth matters for large databases as they try to get data to the RAM as quickly as possible.

Poulin also said that Intel holds a manufacturing advantage that allows it to put more on-chip cache in its microprocessors than its competitors, while delivering power savings, performance and better prices than its earlier chips. However, AMD's Fruehe argued that "customers don't buy nanometers, they buy products."

Transistor size is one attribute of the processor, but the architecture behind it is just as critical, Fruehe said. AMD's chips will size up well on power consumption and performance compared to Intel's upcoming server chips, Fruehe said.

Intel's Nehalem-EX holds an architectural advantage with new features like error correction, but AMD may offer better bang-for-the-buck with its Magny-Cours chips, especially as users migrate from two-socket to four-socket servers, analyst Brookwood said.