Adaptation Distillation: Snippets from dozens of books are thrown in (the title alone comes from two of them.) There is only a brief mention of Stephen being a spy, and the enemy ship is American-made (and thus advanced and well-built) but French-aligned.
Alone in a Crowd: Hollom. Doesn't fit in well with the officers due to his perceived lack of leadership, and can't fit in with the regular crew because he's an officer. The fact that he's shunned basically by everyone makes him the prime target of The Jonah label.
Artifact Title: "Master and commander" is an official naval rank between "lieutenant" and "post captain," and it is Jack's rank during the so-titled book. However, the film takes place later during his career, after he has already made post.
Badass Adorable: Several midshipmen, but cute little Will Blakeney takes the cake. He's a blond teen-aged Pretty Boy who gets interested in science and natural world. And he's a great sailor and officer who can kick some serious ass.
Badass Bookworm: Maturin can't just hold his own in battle; he can do it while nursing a fresh gunshot wound he treated himself without so much as alcohol to numb the pain. Digging a bullet out of your own gut? Pretty damn badass.
Black Comedy: The morning after Hollom commits suicide, there's a service for him. Killick hands Jack a copy of the Bible... which is open to the book of Jonah. Jack gives him an extremely not-amused look and hands the book back before carrying on.
Boarding Party: They manage to trick and successfully board Acheron, but the battle is hard.
Burial at Sea: Midshipman Hollom has a funeral, a service read in his honour, and several lower deck sailors and officers after the climactic battle.
Cool Boat: The Acheron is newer, faster, stronger, and better-armed than the Surprise, by some accounts an "aged man of war".
Aubrey: The Surprise has a bluff bow, lovely lines. She's a fine seabird: weatherly, stiff and fast... very fast, if she's well handled. No, she's not old. She's in her prime.
Chameleon Camouflage: Towards the end the repainting of the hull is pointed out. The re-rigging of HMS Surprise from fully-rigged ship to barque is not mentioned at all.
Chromosome Casting: Justified. Neither the French nor Royal Navies allowed female sailors, and privately owned ships generally considered it bad luck to have women aboard ship. The solitary woman in the movie is a Brazilian lady who's on screen for all of five seconds doing nothing but twirling a Parasol of Prettiness.
Easy Intelligence: "The French have their spies in England and elsewhere... as do we." ...What? You mean a French spy all the way back in Portsmouth when he saw Surprise put to sea, ran out across the ocean to warn the French Captain so he could lay an ambush at just the right time and place? Possible though, as there could have been agents located in South America or other ports where the Acheron could have stopped by. These agents would not necessarily have seen the Surprise put out to sea, but they would have been aware of English man-of-war movements in the area. It is also possible that the French were warned that England had dispatched the Surprise to intercept Acheron, allowing the Acheron to ambush Surprise rather than the other way around.
Empathic Environment: As soon as Hollom is buried at sea, the wind picks up. Depending on how you look at it, either Hollom's spirit has forgiven the crew for their lack of fellowship, or driving him to suicide removed his curse on the ship and they can get on with their duties. Or it was a complete coincidence. Though he said meaningful words right before jumping off the ship, implying he felt he might have actually have been cursed. Ambiguity about such things is a common plot device.
Blakeney: The Captain says we'll get our wind tomorrow.
False Flag Operation: HMS Surprise literally flies a false flag as part of its disguise to lure the Acheron in for the final battle; they do raise the proper flag before actually engaging in combat. Just before, mind you. A second or two, but that's enough for honor.
A common strategy for naval battles of the day. Deception was an accepted tactic, but only to a degree. The rules of battle stated that you could fly false flags or no flags at all up until the guns began firing. At that point, you were supposed to raise your true colors. If you did not and the battle turned south, the crew could all be executed as pirates rather than being given honorable treatment as prisoners.
Foreshadowing: Something bad was bound to happen the second a sailor started trying to kill an albatross.
A Friend in Need: Captain Aubrey has to choose between pursuing his quarry and saving Dr. Maturin's life. Stephen also has to choose to abandon his precious specimen collection, to inform Captain Aubrey the Acheron is nearby.
Good Scars, Evil Scars: Lieutenant Pullings' facial scar is much more disfiguring in the books than it is in the film, but since Pullings' actor is Mr. Fanservice, nobody objects too much.
Grand Theft Prototype: Aubrey's crew takes possession of the Acheron at the end of the movie. Should be noted also that the Real Life HMS Surprise, the inspiration for the ship in the novel, was originally the Unité, a French corvette in service of the French Navy, which was captured by the British Navy, renamed, and introduced into British service.
Handicapped Badass: Will Blakeney, a one-armed 13-year old Little Lord BadassPlucky Middie. Naturally he looks up to Lord Nelson, who also lost an arm. A beautiful moment occurs when Aubrey visits the young Lord Blakeney in his hammock just after he has had his arm amputated. He recommends a book to the young Lord's attention; an account of the battle of the Nile, with several fine illustrations. After some very stiff-upper-lip dialogue, Aubrey departs, leaving Blakeney to leaf through the book, which opens at an illustration of Lord Nelson, minus an arm. Blakeney more than rises to the implied challenge.
Dr. Maturin speculates about evolution decades before Darwin. Though evolution was already being speculated about years before the film is set, by Lamarck and Erasmus Darwin (Charles' grandfather) among others. Darwin's big idea was of natural selection, not evolution. The More You Know...
Jack says something along the lines of "heading home before peace breaks out with France, God forbid". He's not being facetious. Should peace break out, he would have been very likely to be on the shore, on half pay, with no prospects for bettering his situation through taking prizes. Peace, for naval officers not amazingly well-connected, tended to mean near starvation.
In-Series Nickname: Captain John Aubrey's nickname is "Lucky Jack"; his friend Stephen called him that, and also his crew.
Inspirationally Disadvantaged: Invoked by Aubrey. He brings a copy of Lord Nelson's battles to Will, to inspire the new amputee to achieve great things like the great Lord Nelson, who also lost an arm to battle.
Karmic Death: Just about everyone who specifically goes out of their way to be mean to Mr. Hollum ends up dead.
Karmic Jackpot: Saving Dr. Maturin's life and letting him wander around the Galapagos like he originally promised leads Captain Aubrey straight to his prey's front door and a tactical idea made out of Mixed Metaphors and NATURAL PHILOSOPHY!
Knuckle Tattoos: Old Joe Plaice has "HOLD FAST" tattooed on his knuckles. This is a tattoo that was common on sailing ships in the old days.
"The lesser of two weevils". A groaner for Dr. Maturin and the audience, but hilarious for tipsy Captain Aubrey and the other characters present. Jack pestering Stephen to walk into the joke is funny in and of itself. As is Maturin's Lampshade Hanging of the incident; "He who would pun would pick a pocket!"
"After all, surprise is on our side." Their ship's name? Surprise!
Meaningful Echo: Blakeney asking Calamy to not let them sew through his nose in case he dies. Later Blakeney asks to personally take care of Calamy's body and then asking for help as he, having lost an arm, can't do the job on his own.
Nautical Folklore: No luck with a Jonah aboard... or shooting at certain seabirds. The good doctor is rather shocked to find out that his friend the Captain believes it a bit, too.
Not So Different: When Aubrey finds sheet music and a French horn in the Acheron's captain's quarters. Also the enemy captain is seen to have similar problems of keeping personal hygiene (i.e. shaving and combing). Lampshaded at the beginning when Aubrey wonder what the enemy captain's deal is. Maturin speaks his opinion: "He fights like you, Jack."
Oh Crap: The faces of Acheron's crew are priceless when Surprise rises it's true colors.
Aubrey gets one at the end when Maturin is privately lamenting to him that Higgins (who is not a competent doctor) is the only one even somewhat qualified to care for the wounded on the Acheron. When Stephen informs him that the Acheron lost their doctor to fever long before the battle Aubrey realizes that he's been had.
Out-of-Genre Experience: Let's all pause this history and war to have a nature documentary about Galápagos Islands. While perhaps jarring to many in the audience, this sort of thing happened in the books all the time.
Papa Wolf: Discussed. Aubrey says that the French Captain fights so hard that you would think it's personal for him. Did Aubrey kill his family or something?
Aubrey [boarding the Acheron]: "FOR ENGLAND, FOR HOME AND FOR THE PRIZE!"
Aubrey [leading gunnery practice]: "You wanna see a guillotine in Piccadilly!?" "NO!" "You wanna call that raggedy-ass Napoleon your king!?" "NO!" "You want your children to sing "La Marseillaise"!?" "NO!" "Mr. Mowett, Mr. Pullings, STARBOARD BATTERY!" [crew cheers].
During the climactic battle, Lord Blakeney (around twelve year old) is actually in command of the ship at one point and leads a boarding party of adult sailors onto the Acheron.
Calamy is given the mission of freeing prisoners, gets a Heroic Sacrifice moment, and is promoted to Lieutenant posthumously. He died an acting third lieutenant, and his status at death would have been recorded as such on the ship's muster.
Boyle is seen bravely accompanying Blakeney's boarding party, hurling water over the French cannons to douse the fuses and prevent them firing.
Subverted with Hollom, who is nearly thirty, implying he's failed his officer's exam multiple times, and has no hope of further advancement due to his incompetence and lack of leadership qualities.
In book canon, Aubrey is taller than Maturin and Maturin is described as being fairly ugly and scrawny. Paul Bettany is by no means ugly, and quite a bit taller than Russell Crowe. Aubrey is also supposed to be quite fat, but Crowe couldn't put on that kind of weight and still pull the character off, so he ends up being only a bit stout. From the various descriptions given in the book, it seems that Aubrey is more in the nature of being stout and powerfully built than obese as modern readers/viewers would recognize the term.
The enemy ship, in the book the American frigate USS Norfolk, was replaced by a French privateer built by the Americans. The design in the movie was based on the USS Constitution, christened in 1797, it is the oldest commissioned warship still afloat today, and the Norfolk of the book was based on the Real Life USS Essex, which harassed British shipping in the Pacific Ocean during the War of 1812 and seized 15 prizes before she was captured by the British off of Valparaiso, Chile. Word of God is the movie's producers did not have the same concerns that C.S. Forester had when writing the Horatio Hornblower novels: that American audiences would not appreciate the Americans being the bad guys. Instead, they viewed it a sin to not show Napoleon as the true enemy, since only about three books have the US as the enemy. It does mean, however, that instead of planning to take on a 36-gun frigate in the 28-gun Surprise (disadvantageous but doable), Aubrey gets to face a very mean 44-gun heavy frigate with hull construction comparable to a line-of-battle ship, and is completely unable to penetrate her hull in the first engagement. Instead, he has to resort to cunning and audacity.
Roaring Rampage of Revenge: The fight for the Acheron truly turns in favor of the British when the whalers from the Albatross are freed and they take their anger out on their captors. Complete with roaring.
A Taste of the Lash: One sailor gets flogged for disrespecting and bumping into Hollom, his senior officer. Hollom actually said nothing, and got reprimanded by Aubrey in private because lack of leadership causes ill discipline.
The old sailing-master upon boarding the enemy ship, which is covered with bodies, thinks they are done. However... they are not. The battle is about to continue and he's among the first ones shot dead.
Killik is packing up the Captain's silver. "For God's sake don't drop anything!" Next moment a cannonball blows out the bulkhead behind them, knocking them and the silver to the ground.
Title Drop: Included in the Captain's rousing speech.
Aubrey: "... England is under threat of invasion. And though we be on the far side of the world, this ship is our home. This ship, is England."
Worthy Opponent: The captain of the Acheron, seen disguised as the ship's doctor, presumably in order to regain control of his ship at a later date. Mixed with Not So Different, when Captain Aubrey enters the man's cabin and finds it littered with sheet music and a battered French horn.