the obvious answer to your question is: Debian :)
Here i assume, that you are in the lucky situation not to be forced to use the M$ crap, but you asked about it just by inertia.
On Monday 03 March 2014, you wrote:
> Hi all,
> I'm planning on purchasing a big server with about 40 cores and 35TB of
> storage give or take, and I was wondering on which OS is the most
> recommended for Condor - being a system dedicated for it ?
> Microsoft Windows 2008 R2?
> Microsoft Windows 2012 R2?
> Thank you,