Adaptational Attractiveness: Lady Regan in the novel has hideous boils all over her face. In the miniseries, she's an otherwise attractive woman with a facial birthmark.
Adaptation Distillation: Despite being eight hours long, the miniseries had to significantly abridge the 850+ page novel. Most notably, it cut most of the last part of the book, including all of the Henry II/Thomas Becket showdown, and substituted a different ending. Unfortunately, this compression led to some wonky history, which the book was generally good about.
Adaptation Induced Plothole: The Age Lift of Richard in the miniseries means it makes much less sense whenever he doesn't step in to help his sister when she has trouble with an anti-woman culture.
The Atoner: a minor character is a former thief who rescues Jonathon when Tom is forced to abandon him and becomes one of the monks of Kingsbridge. Later, Brother Remigius
Age Cut: The last shot cuts forward 840 years, to show Jack's cathedral still standing in the modern day.
Creator Cameo: Ken Follett as a British merchant living in France, who was friends with Jack's father.
Cue the Sun: Masterfully invoked by Philip to put the fear of God into some quarriers. Later invoked in reverse by Jack with the unveiling of the statue that weeps at night (and for "at night", read "the second the sun crosses the horizon").
Curb-Stomp Battle: Henry vs. Eustace, who's scared and confused by the chaos of battle.
Henry:[cheerfully] Eustace! Eustace! Good to meet you, cousin! [kills him]
Darker and Edgier: The miniseries, in many respects. While it leaves out some of the gorier details of the novel, it also adds some incest to make the Hamleighs more villainous, and changes just about every death in the story into some sort of murder.
Dawson Casting: 28-year old Eddie Redmayne and Hayley Atwell as teenaged Jack and Aliena in the early episodes. Justified by the need to dramatize a story that spans 35 years.
Even Evil Has Standards: While killing the pig boy that Waleran substituted for Eustace, Walter looks distinctly unhappy about it. He still does it, because he's got orders, but he actually hesitates. Waleran too; presumably he thought that the queen would let the boy go when she realised he wasn't Eustace and so killing him would serve no purpose, and he looks genuinely shocked when she orders him executed purely out of spite. The next time we see him he is putting tacks in his shoes while he prays for forgiveness.
GET OUT! Tom to Jack, after he confesses to burning the old cathedral.
Heroic Bastard: Jack, who has to rise above the grief he gets both from the church, and from his legitimate brother Alfred (who for his part resents being The Unfavourite when by law he's his father's only "true" son).
Historical Villain Upgrade: Stephen of England goes from "weak pawn of the nobles" to personally arranging the deaths of his predecessor, Henry I, and his son and heir so he can inherit the throne.
Hollywood History: Several minor changes are introduced in the TV series for no possible reason other than because they are "so medieval". Among them:
Ellen being forced to flee Kingsbridge because she is accused of witchcraft, instead of just because she is having an open relationship with Tom but refuses to marry him.
St. Adolphus' skull being crushed during the destruction of the old cathedral, then promptly replaced with another skull by Prior Philip.
Jack's father having his tongue cut and then being burned at the stake, instead of just hanged.
For dramatic purposes, the miniseries shows both King Stephen and his son Eustace alive in 1156 when they were both dead by 1154. Additionally, the miniseries has Eustace die in battle, when the real Eustace died of natural causes.
Good People Have Good Sex: We cut from Tom and Ellen having passionate, loving sex to Regan and Percy Hamleigh having perfunctory, unpleasant sex. The two even talk strategy during their intercourse.
Philip accidentally invents the futures market some 500 years ahead of time, and Aliena has to convince him that it makes sense.
Also, Tom Builder’s idea of using glass to build cathedrals, which his sons laugh at. Jack later invents stained glass windows... which Philip thinks are a fad.
I Want My Beloved to Be Happy: Martha's apparently been nursing a bit of a crush on Jack ever since she was small, but never pursued it because he was clearly in love with Aliena (and also perhaps because she's essentially his stepsister). This does however cause her to steal Jack's ring so as to have a small piece of him to herself
Kneel Before Zod: Waleran demands this of Philip after he refuses to declare fealty to him.
Ms. Fanservice: Aliena, what with the love scenes and the skinny dipping. And of course the fact that she's played by the lovely Hayley Atwell.
My God, What Have I Done?: William and Waleran have moments when their conscience makes them feel guilty after the fact. Waleren usually scourges himself when that happens, while William fears he's going to Hell.
My Rule-Fu Is Stronger Than Yours: Waleran tries to have Jack arrested on the cathedral site, and Philip invokes sanctuary. Waleran counts that the cathedral is unfinished and thus undedicated, so doesn't count as holy ground. He's Hoist by His Own Petard later when he tries to claim sanctuary himself.
Red-Headed Stepchild: Tom is a redheaded bastard child. Ironically, his stepfather (and stepsister, for that matter) treat him as a member of the family. This treatment is later applied to Tommy, who is also redheaded
Spiteful Spit: "I fear I must now perform an unfortunate familiarity." Waleran to Stephen after he's gotten captured and humiliated by his enemies, and needs Waleran to save him.
Suffer the Slings: William is hit in the head by a slung stone during the attack on Kingsbridge. It knocks him to the ground with a nasty bruise, which is enough to drive his men off, but does no lasting damage.
Alfred and Aliena's wedding and William and Elizabeth's.
Villainous Breakdown: King Stephen has a huge one when he visits Kingsbridge and sees some red paint on a newly finished statue drop on the fake relic of St. Adolphus, causing it to look like the “saintly skull” is weeping blood, then notices that Jack, its sculptor, is the fiery-haired artist boy he was warned about in a vision of Henry I. He has another episode after finding out his son Eustace has been killed in battle.
Villainous Incest: William and Regan. Provides a bit of an explanation for why William acts the way he does; one look at his face when he mother's coming onto him tells you that (1) he's really Squicked out, and (2) this has likely been going on since he was very young. One such overture directly leads to him killing Regan.