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This is one of the major problems people run across when needing to analyze large amounts data (think av software). It's a problem of heurestics as there are almost an infinite amount of ways a program might behave.
Web applications are more easily identifible though, and programs like nexpose, nessus and w3af have quite a large database of web applications and vulenerable versions to be aware of.
Proprietary software is another story and might require disassembling and reversing the backend platform, which would be extrememly tedious and possibly impossible to accomplish