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.
Badass Adorable: Several midshipmen, but cute little Will Blakeney takes the cake.
Female audience members in their late teens onwards may experience varying degrees of I'm Taking Him Home With Me. Please note that TVtropes.org does not condone kidnapping.
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. If digging a bullet out of your own gut isn't badass, I don't know what is.
"I think I'd like to be... a fighting naturalist."
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.
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.
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.
Driven to Suicide: The aging midshipman Hollom, who has no prospects of promotion, is completely lacking in leadership ability, and to top it off gets labeled as a curse on the ship's luck.
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.
Or it was a complete coincidence. This exchange right before Hollom's suicide:
Blakeney: The Captain says we'll get our wind tomorrow.
Hollom: I'm sure of it.
Though he said that 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. The Bellisario brothers love it for instance and it does fit into Real Life because most uncanny events are probably ambiguous in this way.
Enforced Method Acting: Much of the filming was done onboard of the Rose, a modern replica of the 18th century frigate HMS Rose, which was a semi-contemporary of the real HMS Surprise. And all actors were given a crash course on 18th century sea-faring.
During rehersals, all actors were given tags based on whether they are officers or sailors. This enhanced the sense of comradery within each group, and made sure the actors felt that officers and sailors should not mix. Officers actors were also given a nice clubhouse to rest in throughout the filming.
Executive Meddling: Russel Crowe and Paul Bettany learned how to play violin and cello for their respective roles, but were dubbed over in the final cut with professional recordings.
False Flag Operation: The HMS Surpise literally flies a false flag as part of its disguise to lure the Archeron 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.
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.
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 SCIENCE NATURAL PHILOSOPHY!
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.
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.
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...
In another scene 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.
Karmic Death: Just about everyone who specifically goes out of their way to be mean to Mr. Hollum ends up dead.
Lame Pun Reaction: "The lesser of two weevils". A groaner for Dr. Maturin and the audience, but a Crowning Moment of Funny for 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!"
Meaningful Echo: Blakeney asking Calamy to not let them sew through his nose in case he dies. Doubles as a Tear Jerker when 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.
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).
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: Invoked. Aubrey says that the French Captain fights so hard that you would think he is this.
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.
Pragmatic Adaptation: 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 Russel 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 (see the notes on this in the book section above).
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*
., 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.
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.