The Xeon E3 is a server grade processor so logically it makes a better "server" chip. However you also should consider your application. If it is a web based application, with low-medium traffic, you may find it better to go with the i3 and use the money you save to invest in RAM or SSD's. While the Xeon may be the better server processor, that does not mean it is the better processor for your server requirements.
Like it's been said, the Xeon E3 is the more advanced processor and will generally be more reliable, but Helix had a good point - it depends on your needs. That stated, you can find many bargain priced E3V1-V3s these days.
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Which processor models? Which motherboards and memory? It's tough to say for sure, but I can give some general answers. Conventional wisdom would be to choose the E3 in a server environment.
It's not all about the CPU benchmark stat. That's information to be taken with a grain of salt (I can elaborate if necessary.) CPU benchmark is good at giving general representation of how a processor performs but it's a pretty unscientific way of comparing processors. If one out-benchmarks the other by a lot it's probably meaningful. If one out-benchmarks the other by a few hundred points, it might be within the margin of error. The larger the sample size next to the score, the more accurate it's likely to be.
That said...there are other factors in why you should choose the E3. In a nutshell, it probably has ECC memory and the i3 probably doesn't. It's definitely in a server motherboard. The i3 is a toss-up on the motherboard. The E3 probably includes some built in functions that may be useful, including things like hardware support for AES.
If you let us know more details about the hardware we can give a more detailed answer.
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