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Safe Harbor is just a set of additional quality tests that are also targeted against selected 6500 IOSs. If a particular IOS release passes these tests, you have some additional assurance that the IOS is "safe(r)" to use for some critical business functioning.
See http://www.cisco.com/en/US/solutions/collateral/ns340/ns414/ns504/net_brochure0900aecd802c08fc.pdf
