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.
Adapted Out: The Swedish monk Benno of Uppsala was cut from the film.
The Black Death: At the end of the novel, Adso reveals that William eventually died during the Black Death.
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. In the book, Gui has the three transported away, and all three of them are executed elsewhere.
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.
Flanderization: In the film, the transmogrification of the saintly Ubertino da Casale (a minor character) from a 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.
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 (which is English), 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 are 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 quietly of natural causes (he was also older at the time, about 69 or 70) a couple of years after the time in which the movie takes place.
In Which a Trope Is Described: Every chapter of the novel begins with a flowery summary of the events that will be told. One chapter heading is even self-referential, noting how summarizing a plot-heavy chapter in a heading would not be very useful.
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.
Metaphorgotten: Adso asks William about some of the schisms within the faith, and William comes up with a metaphor involving a river that divides into a delta. When Adso still doesn't get it, William admits he's not really good at parables and tells him to forget the river.
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(???)".
Nice Job Breaking It, Hero: If William hadn't deduced that Jorge was the killer, then sure, Aristotle's book on comedy might have stayed hidden, but on the plus side the entire library and every manuscript in it wouldn't have burned down.
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.
I shall soon enter this broad desert, perfectly level and boundless, where the truly pious heart succumbs in bliss. I shall sink into the divine shadow, in a dumb silence and an ineffable union, and in this sinking all equality and all inequality shall be lost, and in that abyss my spirit will lose itself, and will not know the equal or the unequal, or anything else: and all differences will be forgotten. I shall be in the simple foundation, in the silent desert where diversity is never seen, in the privacy where no one finds himself in his proper place. I shall fall into the silent and uninhabited divinity where there is no work and no image.
Occam's Razor: One of William's tricks of the trade, appropriately enough.
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.
In the book the library burns, the book is destroyed and Bernardo gets away with the torture and unjust execution of three people. This was lightened up a little for the movie.
History buffs and bibliophiles familiar with the period will 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 Guis-this is Hollywood History, as the real inquisitors rarely prosecuted any suspected witches, while most actively disbelieved in witchcraft.
Satellite Love Interest: Taken to an almost comical extreme with the girl, at least in the film. She has no name, no dialogue except for moans during sex, and virtually no characterisation beyond throwing herself at Adso, which she immediately does upon the very first time they meet, without having interacted with him in any way beyond the act of intercourse.
Secret Path: The only unguarded way into the library is various secret passages.
Serious Business: The abbey is hosting a council made up of various factions of the Dominican and Franciscan Orders to debate the burning issue: Did Jesus own his own clothes? In the film, this is used for comedy; in the book it is always clear that they are really discussing the church's approach to poverty and wealth, and that the debate is therefore highly political and momentous.
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.
Sherlock Scan: William of Baskerville, such as at the beginning, when he meets people from the monastery and describes to them the horse they're looking for, though he never saw it.
William also later lampshades and deconstructs this technique as being rather reliant on lucky guesses.
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. In the movie, William has a line that could be rearranged as "Elementary, my dear Adso" (like the famous Beam Me Up, Scotty! relating to Sherlock Holmes).
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.
William: Certainly she is a girl from the village who, perhaps not for the first time, grants her favors to some lustful monk out of hunger, and receives as recompense something for her and her family to eat.
Adso: A harlot!
William: A poor peasant girl, Adso. Probably with smaller brothers to feed.
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.
Title Drop: The postfacium quote, the last line of the book. The movie however doesn't say it outright but implies the girl was the rose with its last line, as Old Adso muses that he never learned her name.
Torture Always Works: Discussed and defied by William who used to be an inquisitor, but avoided using torture. He explains that people under torture say not only what the inquisitor wants, but also what they imagine might please him. Later, when Bernardo Gui interrogates the cellarer, the threat of torture is enough 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.
The Unintelligible: Salvatore, played by Ron Perlman, talks in an idiosyncratic mix of Latin, Italian, English, French and Spanish. Even so far as the words can be understood, his ramblings don't seem to make much sense.
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).Translation "Repent! Watch out for the dragon that cometh in future to gnaw your soul! Death is supreme. You consider the Apocalypse. Out there, we have the devil, as ugly as Salvatore".
Villain Teleportation: Jorge's ability to get in and around the library unseen. Handwaved in the film, as William muses that Jorge must have flown to reach the library before them. Jorge then says that he took the short route.
Wham Episode: The third day. Adso finally learns something about Fra Dolcino! Also he gains "carnal knowledge" of some random young lady! And, by the way, Berengar dies.
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".