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Well, there's a lot of multi-processor linux servers out there - even using old style one 'core' per chip. On that basis I'd think linux will be fine with a multi-core CPU. I like solaris myself - but linux has been around for a couple of decades now.
Because I don't know what you intend to run, what might be the bottleneck of the system. In my world (database land) it's rare that the disk systems can keep more than a few CPUs fed. But that's partly because of the way the systems are set up, and how the queries are written (often badly).
So getting back to your system. Can you define
- how big your program is
- how big your data set is (will it fit in memory... might it fit in CPU cache)
These are the factors drive your decision, ie to spend on faster memory or more cores, or less cores with more cache etc.
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