"They are called dogwatches because they are curtailednote the dogwatch (a naval workshift at either 4-6 pm or 6-8 pm) is only 2 hours long, shorter than the usual naval watches, which are 4 hours." It's still being referenced toward the end of the series (the joke itself may soon grow old to the reader, but the fact that Jack cherishes the old pun and will roll it out for any unsuspecting new character is always amusing).
After a day-long running battle a French ship is sunk by Jack Aubrey. The French officers are entertained by Jack & Stephen at dinner that night. When they are served spoiled, burnt soup it is treated as far worse torture than the battle. "Dipping their spoons they submitted to the horrors of war."
Stephen acquires a sloth in South America, and it immediately befriends everybody aboard. Except Jack, who for some inexplicable reason gets rebuffed- the poor thing cried when it first saw him. When he finally resorts to feeding the sloth bits of ship's biscuit soaked in rum, he soon wins its friendship but ends up turning it into an alcoholic. Thus leading to a line found nowhere else in literature: "Jack, you have debauched my sloth."
Or the time in Post Captain when Stephen came on board, wearing a truly bizarre bee-keeper's suit and carrying a hive of bees (which inevitably got loose, to the dismay of Jack and everyone else except Stephen.)
Aubrey: Are you saying that there are sixty thousand bees loose in my cabin?
Maturin: No, no! Half that number at most. Less.
In The Mauritius Command, once the titular task force is finally all together at the Cape:
Stephen (to Jack):Bonden, Killick and some others are aboard the Nereide, and wish to return to you. All tastes are to be found in nature, we are told; and it is to be presumed that they like the brutal, arbitrary, tyrannical exercise of power.
Made somewhat less funny by the fact that the Nereide's captain, Corbett, is the tyrannical one, to the point of having Bonden whipped for leaving one of its guns insufficiently polished.
Or the time that Stephen adopted a wombat who ate Jack's best dress hat. Memorable enough that it gets a mention the next time they visit Australia, years and years later.
The aforementioned incident of Jack pressing his own creditors' enforcers.
"What's that? You're going to arrest me for debt? No actually I think you're going to work for me for the next year or so. Hope you don't suffer from seasickness!"
Towards the end of The Fortune of War, Jack and Stephen and Diana slip out of Boston Harbor in a fishing scow. There is exactly one skilled seaman on board (i.e. Jack), and frustration ensues.
Stephen: The moment you are afloat you become pragmatical and absolute, a bashawnote pasha, i.e. autocrat—do this, do that, gluppit the prawling strangles, there—no longer a social being at all.
Any encounter Jack has with "Awkward" Davis, a brutish, unpleasant fellow who is not a particularly good seaman but who has an unbreakable claim on Jack's loyalty considering that Jack once saved the man from drowning.
The situation repeats itself after Jack saves Ponto the mastiff from drowning in Treason's Harbour, although where Davis was a run-of-the-mill Klutz, Ponto is borderline lethal even (or perhaps especially) when he's in a good mood. It doesn't help that he shows his gratitude by cornering Jack in a Murano glass shop.
Or the time that, when inspecting his crew, Jack found a seaman who had sold off literally almost all his kit to buy liquor and was down to one shoe. He unleashes a memorable smackdown on the unfortunate midshipman whose division the wretched fellow is in.
Then there's the time that Jack decided to quiz the midshipmen under his charge on their Biblical knowledge, specifically Abraham. Each answer he gets is more preposterous than the last, and the unlucky final middie gets a good tanning with a knotted rope's end from Bonden for his impertinence.
The first time we see Stephen let out a full-bellied laugh (or his equivalent, anyway; it's described as a dry, creaking sound) is when Jack informs him that he intends to preach a sermon to the crew at the next Sunday divine service.
Jack's opinion on Odysseus. "Twenty years to sail less than a hundred miles? He was no kind of seaman."
Another one from Post Captain, "Jacques Aubrey"'s fake French identity papers. "Born 1 April 1066 at Bedlam, London. Father's profession, monk: mother's, nun. Mother's maiden name, Borgia, Lucrece." Sadly, the speaker gets cut off before he can get to "Etienne Maturin".
In The Fortune of War, Aubrey is wounded, and he and Maturin are captured by the Americans and taken to Boston. Maturin asks an American surgeon about improved accommodations for Aubrey, and the surgeon recommends a hospital that sounds excellent but is used mainly as a mad-house because of its owner's unpopular opinions and penchant for hiring Irish help. His remarks include some well-meant but highly unflattering statements about the Irish, right to the face of the half-Irish Maturin, until a semi-conscious Jack blurts out, "Never mind Maturin, he is an Irish Papist himself, ha ha ha! Drunk as a Lord every morning by nine o'clock, and never a shoe to his name." The surgeon is so mortified and apologetic that even Maturin's oft-dangerous temper is never roused.
While recovering in the mad-house mentioned above, Jack amuses himself by listening to the insane ramblings of his fellow-patients and telling them wild tall tales in return. When an American interrogation team comes to question him, their leader is an odd-looking man with an unusual name, so Jack mistakes them for more lunatics, and makes bizarre claims and confesses to outrageous crimes to the point where the interrogators think he is drunk.
Most sequences where Stephen has to get onto a ship would most likely involve him falling off a ship in one hilarious way or the other. It's a testament to their friendship that Stephen still agrees to volunteer to be Jack's ship surgeon after so many falls.
Aubrey: Why, you are all wet. Surely you did not fall in, like a mere lubber?
Maturin: I did not! The sea it was that rose. note True, this time around in The Ionian Mission—Maturin had hoped to leap aboard, but missed, and found himself clinging to the tumblehome side of the rocking, swaying ship at the top of its rise; when it came back down...
Just before crossing the Suez isthmus in Treason's Harbour, Stephen compares notes with a local scholar on the wildlife of the Nile delta, including the majestic eagle owl. At about the same time, the Turkish odabashi, who happens to speak English, is filling the warrant officers' heads with terrible stories of the spirits and ghouls that lurk in the desert—one of which has horns and glowing orange eyes, and makes strange hooting noises. (For the record, the odabashi appears to believe every word of what he's saying, although it's hard to tell for sure.)
And then. A hyena calls outside, scaring the daylights out of everyone...followed immediately by a strange hooting noise, and the order to strike the tents and move out for Suez. In the dark. On foot.
Jack has some difficulty composing his report on the Suez/Red Sea mission.
Listen to this, Stephen, will you? "Sir, I have the honour to acquaint you that pursuant to your orders of the third ultimo I proceeded to Tina with the party under my command and from thence to Suez with a Turkish escort, where I embarked in HEI Company's sloop Niobe and, having eventually taken the Turkish contingent aboard, proceeded in adverse weather to the Mubara channel...where I made a complete cock of it." Now the point is, how can I best say that without looking too much of a fool?
In The Letter of Marque, Jack trains the crew of the Surprise for a lightning harbour raid on the French coast, in a secluded bay. Naturally, this includes midnight boarding drills and gunfire. The reactions of the civilian dwellers on shore — many of whom had never seen a man-of-war — are hilarious, some mistaking the Surprise for a pirate ship come to carry them off. Even better, a revenue cutter, suspecting them of smuggling, tries to investigate but gets caught on a sandbar, and has to be towed off by Aubrey's crew.
When their ship is captured by a Spanish frigate who insists they surrender and be boarded, Stephen cheerfully asks if they have anyone who knows how to deal with the plague, because nobody on his ship has a clue. The Spaniards change their mind about boarding and insist that they go away. Far away.
Babbington being promoted to acting-lieutenant, only to remorsefully admit to Jack and Stephen the truth about the fate of Stephen's rats.note The doctor had been feeding madder dye to the rats, to see if it would build up in their bones or other tissues; after finding out that some of the midshipmen had eaten them before he could dissect them, he got revenge by dosing the boys with an "antidote" that presumably had unpleasant intestinal effects.