In the final sketch, when the studio audience charges the set, they are led by a plant in the audience: Ian MacNaughton, the show's producer, who makes various appearances throughout the show.
In the sketch in the submarine, Michael Palin is obviously pretending to knit, while Terry Jones is actually knitting properly.
Mr. Pudifoot, The Man Who Says Things In A Very Roundabout Way, is inspired by Graham Chapman's romantic partner David Sherlock. Sherlock was notorious for his tendency to digress while talking, something John Cleese found particularly hilarious. This quirk also inspired (Miss) Anne Elk, the woman with a new theory about brontosauruses (and what it is, too), played by Cleese in their third season.
In the Coal Miner sketch, the Foreman asks the question: what is the name of the section between the triglyphs in the frieze section of a classical Doric entablature. To which the Royal replies: No idea, sorry. The answer is that the square recessed spaces between the triglyphs on a Doric frieze, are called "metopes".