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Besides the monetary cost, there's the opportunity cost of dealing with licenses in the first place. Part is compliance (Does your company have current licenses that cover every bit of software on every virtual machine on every developer laptop? Can you prove it?) and part is procurement (Do you get the plan with free upgrades, or do you buy new? Will you need enough licenses over the next two years that you should get a site-license or is it cheaper to stick with single user licenses?).

The cost of the Windows OS itself it not the real cost. SQLServer gets costly as you grow out, but not nearly as bad as Oracle.

http://www.microsoft.com/sqlserver/2008/en/us/pricing.aspx

Yes, BizSpark makes it free, but that basically locks you into the platform long enough for you to rely on it before you start paying those prices.

Correction: it doesn't matter for some workloads.

This old classic applies to business models as well as software: http://www.joelonsoftware.com/articles/FiveWorlds.html