Adaptation Distillation: The book is a detective mystery interwoven with 500 pages of incredible detail of the religious and political schism in the church that is nearly inscrutable to anyone without a post-graduate degree in Theology and 14th Century Political History. (Or, reasonably arguably, anyone but Umberto Eco.) The movie drops most of the Theology, History and Politics in favor of the detective story.
A Man Is Not a Virgin: Adso gets to have one fling before recommitting to chastity; William, his mentor and supposed guardian, says something along the lines of, "Way to go, kid."
Averted with William, who explicitly admits to Adso that, unlike him, he has never tried "that sort of experience."
Asshole Victim: In the movie, Bernardo Gui's cart gets pushed off a cliff by angry peasants, causing him to fall on a spiked thing which kills him. Your heart bleeds for him.
Brick Joke: (Novel only.) In what seems to be another example of Did Do The Research, William discusses an Arabic treatise on hydrophobia (rabies) in dogs in passing. It comes up again during the trial of the cellarer when William claims this is what he was discussing with a murdered monk, going into great detail about how the text describes the twenty-five symptoms of hydrophobia, with which Bernardo Gui is surely familiar. This swipe is a pun on Gui's order, the Dominicans- "domine canes", God's dogs.
Burn the Witch!: In the film, Brother Salvatore and Brother Remigio are burned at the stake as scapegoats by Father Bernardo Gui, leader of the Inquisition. Gui also tries to burn a local peasant girl, but in the film she is rescued by rebellious peasants who manage to kill Gui in the resulting chaos.
Unfortunately, her two fellow "heretics" don't get rescued. Adso was a trifle specific in his prayer.
In the book, Gui prevents this from happening by simply having the three of them transported away and executed elsewhere, where no rescue attempts can occur. (Gui was a historical person, and he was not killed by peasants).
Camp Gay: Brother Berengar, with foul consequences.
Double Standard: Rape—Female on Male: The peasant girl jumps on Adso, but after the initial shock he seems quite willing — and even enthusiastic. He's a young man who probably struggles even against the desire to masturbate. Few would have more self-control in that situation. William later says that in Adso's place "even a father in the desert would have damned himself".
The Dung Ages: This is how the monastery is portrayed in the movie.
William has one considering the secret of the library. Adso remembers how Salvatore said "tertius equi", which is Canis Latinicus for "The third of horse" (when he meant "the third horse"). William concludes: "the first and the seventh of the four" really means "the first and the seventh of the word four", and "four" is "quatuor" in Latin, so you have to push the letters Q and R!
They had a minor one earlier, when Adso dreamed a story similar to the "Coena Cypriani", a kind of Bibleparody. Which helps William to remember that there was a book in the library consisting of four texts, one of them a comment for the Coena Cypriani, another one the book they're looking for.
Fake Nationality: Everyone besides Sean Connery. Not counting the lack of Italians (even the girl is Chilean), Adso (Austrian) and Bernardo Gui (French) are played by American actors.
Flanderization: The transmogrification of the saintly Ubertino da Casale (a minor character) from well-educated, decent, pious (if slightly fanatical) old man to a creepy, obtuseButt Monkey who hits on Adso and is ridiculed by William. Note that the poor guy actually existed.
Foe Yay: invokedLampshaded by Adso in the book as he follows the last dialogue between William and Jorge.
William has to choose between burning to death to save as many books as he can, or abandoning the library.
Getting Crap Past the Radar: At one point, Adso describes how William angrily spits out a one-syllable word in his native language (remember, William is British), and comments that he luckily didn't understand the word, because it sounded very much like it means something naughty...
Gonk: The Abbot, the Greek translator, and Adelmo are pretty much the only three of the Benedictine monks who is not frightfully ugly. The worst is undoubtedly Ron Perlman's Salvatore, who doesn't even look human.
Impaled with Extreme Prejudice: Bernardo Gui in the film. This didn't happen in the book or in Real Life, in which he died a far less cheesy death a couple of years after the time in which the movie takes place.
The blind monk Jorge of Burgos is a shoutout to the (blind) Jorge Luis Borges, an important literary influence for Eco.
Medieval Morons: William himself and the sensible Adso make everyone else look fanatical or dumb, at least in the movie. In the novel, many people show a great deal of scholarly knowledge and expertise, but William is about the only one who can escape beyond the stagnated and fundamentalist nature of medieval learning.
Mind Screw: How to access the secret room in the library. "The hand over the idol?/image?/mirror! should move (how exactly?) the first and the seventh of the four(???)".
No Name Given: The girl Adso has sex with. He mentions that he couldn't even "lament and call out the beloved’s name" (as he read in romances of chivalry) when he learned that she's going to die, because he never learned her name.
Out-of-Genre Experience: In-genre for the book, but the film pauses the action for a theological debate between the progressive, liberal Franciscans and the Vatican emissaries over the question of whether Jesus owned the clothes that he wore.
Playing Against Type: Sean Connery, one of cinema's most iconic male sex symbols, plays a virgin Celibate Hero who apparently considers women to be foul creatures purposefully designed by God to tempt man. (The book shows the character specifically questioning the latter very common belief, so the interpretation may not be fair for the movie either.)
In the book the library burns, the book is destroyed and Bernardo gets away with the torture and unjust execution of three people. This proved to be too dark for the movie, in which, at least, Bernardo dies and the girl lives.
History buffs and bibliophiles familiar with the period might consider will definitely consider the burning of the library to be an outright Downer Ending. (Eco himself pointed out in the Apostilles to The Name of the Rose (essentially a director's track book) that having a library in that period and not having it burn down would have been absolutely unrealistic.)
Red Herring: The connection between the various deaths and the seven trumpets of Revelation turns out to be a coincidence after all. When this theory is discussed openly, the killer decides to run with it, which complicates things further.
Sadistic Choice: Gui insists William, a former victim, serve as a judge in The Inquisition: In the book, William is a former Inquisitor, who wants nothing more to do with it; the movie shows that William refused to convict a witch and got marched out and judged by Gui.
Shaggy Dog Story: If you read carefully and think about it, you'll notice that this is a detective story where the detective isn't very successful - he even admits it near the end-, and the Big Bad is never brought to justice.
Further, the name "Baskerville" is an obvious allusion to the Sherlock Holmes novel, The Hound Of The Baskervilles; Adso's name sounds very similar to Watson's; and Adso's description of William of Baskerville in the "Prologue" is taken almost word-for-word from Watson's first description of Holmes in A Study in Scarlet.
Jorge, the blind librarian, is a clear reference to Jorge Luis Borges, the Argentinian author who went blind, served as the director of Argentina's National Library, wrote a story about a labyrinthine library, and is generally credited as a stylistic influence on Eco and probably hundreds of other genre-bending postmodernist authors.
Someone lucky enough to have read Borges's short story Death and the Compass will see the connection to this story clearly
You are the Devil. Yes. They lied to you. The Devil is not the Prince of Matter; the Devil is the arrogance of the spirit, faith without smile, truth that is never seized by doubt. The Devil is grim because he knows where he is going, and in moving, he always returns whence he came. You are the Devil, and like the Devil, you live in darkness. If you wanted to convince me, you have failed. I hate you, Jorge, and if I could, I would lead you downstairs, across the grounds, naked, with feathers stuck in your asshole and your face painted like a juggler and a buffoon, so that the whole monastery would laugh at you and be afraid no longer. I would like to smear honey all over you and roll you in feathers and take you on a leash to fairs, to say to all: He was announcing the truth to you and telling you that the truth has the taste of death, and you believed not in his words but in his grimness. And now I say to you that in the infinite whirl of possible things, God allows you to imagine a world where the presumed interpreter of the truth is nothing more than a clumsy raven who repeats words learned long ago.
Torture Always Works: Averted. William used to be an inquisitor, but avoided using torture. He explains that poeople under torture say not only what the inquisitor wants, but also what they imagine might please him. Later, when Bernard intorrogates the cellarer, the threat of torture is enogh for him to admit that he committed all the murders (which he didn't do).
The Tower: The hidden and locked library looms over the monastery, tall, dark, labyrinthine and foreboding. Eco helpfully draws a diagram of it for readers.
Salvatore: "Penitenziagite! Watch out for the draco who cometh in futurum to gnaw your anima! La morte è supremos. You contemplatum the apocalypsum. Là-bas, nous avons il diabolo, ugly comme Salvatore" (in this scene).
Well-Intentioned Extremist: Jorge wants to destroy the last edition of the Poetics of Aristotle in the film, because he feels that it will teach men to approach all matters with laughter and kill fear of the devil and thus, in his mind at least, render men irreligious.
Your Mom: During their final argument about laughter, Jorge mentions a story about a Minorite, who fell on the ice, and when someone mockingly asked him, if he wanted to lie on something better, he answered: "Yes, your wife".