We currently obfuscate all our output, even though we are a small outfit who sells specialist software to a small number of clients.
We made this decision for one simple reason - we discovered a disgruntled ex-employee was actively approaching our clients requesting binaries - there was some some concern he was intending to reverse engineer newer features in order to offer competing functionality.
Of course he is still able to do this if he uses the software, but there is no reason to make it easy for him.