Doctor Stephen Maturin performing an advanced trepanning operation on 'Old Joe' Plaice after the Acheron's first attack leaves him with a shrapnel wound that has fractured his skull and a near absolute chance of mortality. Not only does the doc ensure he doesn't die but the grizzled sailor eventually regains his voice and returns to full fitness! A "physician he is" indeed.
The author of the books the movie is based on often opened with apologies. Typically, he apologized for anachronisms (including Eau de Toilette in a scene 10 years before it appeared, or putting a naval battle before the grape harvest when it was known to have occurred AFTER the grape harvest...), but on a few occasions he apologized for toning things down. In his own words, "When one is writing about the Royal Navy of the eighteenth and early nineteenth centuries it is difficult to avoid understatement; it is difficult to do full justice to one's subject; for so very often the improbable reality outruns fiction. Even an uncommonly warm and industrious imagination could scarcely produce the frail shape of Commodore Nelson leaping from his battered seventy-four gun Captain through the quarter-gallery window of the eighty-gun San Nicolas, taking her and hurrying on across her deck to board the towering San Josef of a hundred and twelve guns, so that 'on the deck of a Spanish first-rate, extravagant as the story may seem, did I receive the swords of the vanquished Spaniards; which, as I received, I gave to William Fearney, one of my bargemen, who put them, with the greatest sang-froid under his arm'"
Captain Aubrey's toast. "Here's to wives and sweethearts—may they never meet!" especially for those familiar with the books.
This was an actual toast said in the officers' mess on Saturdays. Typically, one officer would say the first part and the second would be said by the youngest present.
Maturin gets an unmitigated MoA to himself for the last third of the film, when he operates on himself to remove a bullet. Compounded by his pausing to ask Jack Aubrey (who is certainly no shrinking violet) if he, Jack, is all right.
"LET FLY!" The Surprise can achieve some awesome speed.
Lucky Jack's Rousing Speech to the whole crew, before their assault on the Acheron.
When the HMS Surprise drops her disguise as a whaler. The ship halts, the marines come out from hiding under canvas, and the cannons come out to blast the Acheron's mast to splinters. After the main mast topples, the Surprise sweeps in behind and blasts the Acheronfrom behindwith her other battery. A CMoA for the entire ship.
Also, the one-armed 12 year old Midshipman Blakeney countering an attempted hull breach with one of his own and subsequently leading the second ship boarding party.
Jack beasting his way through the mid-decks with sabre, pistol, grenades and anything else at hand, he's such a whirling dervish of destruction that eventually the French sailors would rather flee and surrender rather than fight the Captain of the HMS Surprise.