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It is also more frequently used than captain with privately-owned noncommercial vessels, such as small yachts and other recreational boats, mostly in cases where the person in command of the boat is likely not a licensed or professional captain, suggesting the term is less formal.
In Navy/Marine Corps and merchant naval slang, it is a term used in reference to the commanding officer of any ship, base, or command regardless of rank. It is generally only applied to someone who has earned the speaker's respect, and only used with the permission of the commander in question.
Skipper RNR was an actual rank used in the British Royal Naval Reserve for skippers of fishing boats who were members of the service. It was equivalent to Warrant Officer. Skippers could also be promoted to Chief Skipper RNR (equivalent to Commissioned Warrant Officer) and Skipper Lieutenant RNR.