While most of my experience over the last 17 years has been specific to businesses with under 500 locations only requiring a typical point of sale system, I have worked with a few businesses that had more complex needs specific to warehouse management, production, distribution, and transportation logistics. Usually these business had under 50 locations but are part retail/part wholesale/manufacturer and found that most point of sale systems fell short of what they needed.
Not cheap by any means, the Microsoft Dynamics family includes the Dynamics NAV and Dynamics AX software solutions which are true enterprise solutions. The nice part is that these software programs are also modular based so you can pick and choose what modules are needed for your business or organization.
These are solutions that require a high level of help with training and deployment so finding the right Dynamics Partner is critical and I have worked with a few partners that I might be able to recommend (or you can contact Microsoft directly as well).
Please visit my contact page for information on how to reach me for unbiased point of sale advice.