Abhorrent Admirer: Grunhilda, to Gaius. Vivian, to Arthur (by the end of the episode at least).
Aborted Arc: Why Aithusa sided with Morgana was never explained.
In Series 2, Merlin tried to stop Mordred fleeing from Camelot's army. In response Mordred kills the two soldiers chasing him and coldly tells Merlin via telepathy that he will never "forgive or forget" that. When he comes back in Series 5, he's completey forgotten about it.
For the first two series it was treated as a pretty big deal that a) Arthur was born of magic, and b) he didn't know about it. It was built up to be a revelation that would shake-up the show, particularly in regards to Arthur's views on magic. The likes of Uther, Nimueh, Gaius, Merlin, Morgause and the ghost of Ygraine all play a role in this mini-drama, but once Merlin convinces Arthur that the ghost he saw of his mother (who tells him the truth) was simply a trick, the entire thing is dropped and never brought up again (unless you count a throwaway line in series 4).
The first two series also setup a growing sense of animosity between Merlin and the Great Dragon, with Merlin often refusing to follow the Dragon's instructions based on his own personal sense of right and wrong. It seemed like it was heading for a schism between the two characters, in which Merlin would decide to follow his own path instead of blinding following destiny (especially regarding some of the incredibly dodgy stuff the Dragon tries to get him to do), but at the start of series three this is all forgotten, and Merlin never questions the Dragon's word again.
Aborted Declaration of Love: Arthur seems to be on the verge of telling Guinevere that he loves her in the series three finale. However, she interrupts him after he makes the mistake of saying "if I never see you again..." which only compels her to insist that they will meet again.
Abusive Parents: Uther. It is obvious that many of Arthur's insecurities stem from being raised by an emotionally distant and cold father. The same could be said for Morgana and her emotional, mental and psychological issues. Although Morgana was never really mistreated by Uther, the way Uther talked about magic users like Morgana definitely contributed to Morgana's Face-Heel Turn in season three.
Also Colin Morgan has portrayed a total of three different characters including standard Merlin, Dragoon/Emrys, and Dolma. How he manages to pull off making all three different characters with different quirks is amazing.
Action Dad: Uther. He's always involved in the action in regards to Camelot.
Adaptational Villainy: Obviously it depends on what source material you're working with, but the likes of Morgana, Morgause, Mordred, Nimueh and Agravaine can be portrayed much more sympathetically in various legends and other adaptations than they are in this series.
Adorkable: Merlin and Gwen (especially in her early appearances).
In the series 4 premiere, Gwaine and Percival trying to swipe a chicken.
Mordred rides a horse in reverse because the knights told him it's tradition.
Adult Fear: Think about this from Gaius's point of view. Merlin is like a son to him. He probably fears more for Merlin's life than Merlin himself does. A lot of the time, he doesn't even know the whole story of what Merlin's up to. So it makes perfect sense that he's constantly pestering Merlin about keeping his magic secret- he's terrified that Merlin isn't taking his warning seriously enough, and he knows that if Merlin is caught in the act just once, he's as good as dead.
Think of all the times when Gaius has to lie and say Merlin's at the tavern. He covers for Merlin, but half the time even he doesn't know where Merlin is or what he's doing. He's just hoping that, whatever the situation, Merlin's going to make it back home.
Cast members expressly said that we could expect most of the conflicts of series 5 to center around Adult Fear types of issues, and that it would be “a lot darker” in tone. They were right.
Adults Are Useless: Uther's the bloody king, for crying out loud. Though he apparently was very good at killing everyone with magic.
Subverted with Gaius. Played straight with everyone else even if, in typical showbiz fashion you shave a few years off the actors real ages they're still in their late teens (Merlin) to mid twenties (Gwen) so maybe "Authority Figures Are Useless" would be more accurate.
All Just a Dream: Episode 3x10 opens with Gwen becoming Queen of Camelot with Arthur as king, but it is shown that it is just a dream of Morgana's though this dream comes true in the series 4 finale.
Almost Kiss: Arthur and Gwen in The Castle of Fyrien and at the end of Queen of Hearts. They actually do manage to get there earlier in the latter episode, but are interrupted just as they're getting started.
Always Save the Girl: Arthur, Merlin and Lancelot have all been willing to give up what is most important to them in order to save Guinevere; respectively, his entitlement to the throne, his magical secret, and his life.
Always Second Best: Arthur and Lancelot have this mentality in regards to each other, each believing that the other is "the better man" in everything from their skills in combat to how Guinevere feels about them.
Ambition Is Evil: Morgana's thirst for power and to become Queen of Camelot and gain entitlement to the throne at any cost, including trying to kill her own half brother (Arthur) and turning against her own former best friend (Gwen) is simply nothing but pure evil. Morgana's hunger for power turned out to be her ultimate downfall.
Anachronism Stew: It pretty much turns Anachronism Stew Up to Eleven, but somewhat justified in that it's probably not set in our timeline at all (though this may have been Jossed by the closing moments of the Grand Finale). When the creator was criticized for it, he pointed out that it isn't supposed to be historically accurate. People complain about the tomatoes, he said, but oddly enough no one's commented on the dragon.
Knights in plate armour and huge stone castles in pre-Saxon England.
Gaius' medical knowledge being far too advanced for the time period.
Gwen's kidnappers use chloroform. I mean, "compound of hog's wart."
In Lady of the Lake, Arthur appears to be having pre-packed deli meat for breakfast. Oddly enough, in the same episode, when Merlin steals the original meal and replaces it with food from a cupboard in Gaius's quarters, one of the components is a shriveled, close-to-rotten whole apple... an uncomfortably realistic detail of medieval life.
Parodied in the 2009 Children in Need special, in which the kingdom is invaded by "magical items" like microwaves, hairdryers and mobile phones. See it here.
French chivalry in the middle of dark age Britain. Although you can't blame them for that one, that was in the original myths.
And let's not forget the infamous aluminium beer cans on the table in Lancelot and Guinevere.
As well as the coat hangers, which didn't appear in that form until the 1900s.
Anti-Hero: Almost everyone can be considered Type III, due to the show being in the Middle Ages where killing and not losing sleep over it is the norm. Adjusting, most of the knights and Arthur are Type I or Type II with a side of Hero Antagonist.
Anti-Villain: Several of the villains in the series. Uther was a genocidal tyrant but he also genuinely loved his children and cared about his people. Morgana, Mordred, and most of the Villains of the Week attack Camelot because of its laws that persecute them.
Anyone Can Die: The first three episodes of Series 4 see the deaths of Morgause, Lancelot and Uther.
Series 5 kills off, in order: Elyan, Mordred, Gwaine, Morgana and Arthur.
Arch-Enemy: Merlin to Morgana and vice versa. According to The Great Dragon, Morgana is the dark to Merlin's light and the hatred to Merlin's love.
Arc Symbol: The Round Table. Hints of it turn up throughout the first four seasons - Arthur gathers villagers in a circle around him and tells them that they're all equal, his knights form a circle around him when he asks for volunteers to help him fight the dragon; and he gathers all his closest allies around a circular stone table while they're on the run and tells them that it symbolizes the way they all worked together. Finally appears in season five in the hall of Camelot Castle, with everyone gathered around.
Army of the Dead: Used several times. One time with skeletons, one time with technically undead (the Cup of Life was used to make an army immortal, and they counted as undead), and one time with actual spirits. In the latter case, it wasn't so much an army as a swarm of angry ghosts attacking at random, but the spirit is the same.
Despite centuries of characters added with the retelling of the Arthurian myths this TV show opted to still add the character Gaius who was made up for the series.
In The Gates Of Avalon Gaius states that a staff had Ogham script on it, then show the page. The script shown does carry the same format as Ogham in that there is a line connecting all the letters and it is a series of lines, but the props department then embellished the script by making it much more TV friendly (most of Oghams' letters are a series of 1-5 dashes connected on a line, the script shown only had the vaguest basis on Ogham.
In To Kill The King Gaius talks about a magic stone that has been lost for 1000 years. Said stone has writing on it, in Anglo Saxon runes, which are from two hundred years after the time period of Arthurian myth. 1000 years before THAT the writing the writing would have been in the Euboean alphabet. Or at least cuneiform.
Aww, Look! They Really Do Love Each Other: Arthur and Merlin may insult each other like no tomorrow, but deep down, they really do care for each other and are willing to sacrifice themselves to protect the other.
Ditto for Arthur and Morgana in season one.
Automaton Horses: In a sense. They're used a lot, but we never see them getting groomed or fed or watered.
Merlin mucking out the stables is a running gag, though. In Aithusa Merlin has to forgo his own dinner to feed the horses. And in Sword in the Stone Part 1 Merlin has simpleton! Arthur rub down the horses. So caring for the horses is definitely there, but Law of Conservation of Detail often Hand Waves it.
Back for the Finale: At the end of series three we get reappearances from Lancelot, Elyan, Gwaine and Freya.
Bad Boss: Arthur can appear as it towards Merlin, but it's mostly for comedic effect. Morgana to Agravaine, and it's played seriously.
Badass: Numerous characters in the series could qualify. But Merlin is the most powerful character in the entire series, so he qualifies the most.
Badass Boast: In Aithusa, when Gaius' power hungry and traitorous former pupil scoffs at Merlin's assertion that the Dragon's egg should not be used as a tool, Merlin comes up with this gem just before he blasts him into a wall. The Oh, Crap look on the man's face just makes the scene.
Merlin: I am the last Dragon Lord. And I am warning you - leave this egg alone.
Badass Bookworm: Merlin. He reads and researches alot and spends a lot of time with his nose in a book when he is not saving Arthur or doing chores for Gauis.
Although it's debatable as to what extent they could be called "bystanders", Sir Owaine and Sir Pellinore in Excalibur take up Sir Tristian's challenge to a duel in order to prevent Arthur from doing so, and go to certain death as a result.
Badass Cape: The red capes with a embroidered golden dragon of the Camelot knights, though it ironically makes them a literal Red Shirt Army.
Balancing Death's Books: Basic rule of the Old Religion is a life for a life (it seems that the life of the person most important to the one who asks will be taken, hence Igraine dies because of Uther's request for a son, and Hunith nearly dies because Merlin asks for Arthur to be spared).
In the episode "Goblin's Gold", the title goblin can turn into a mote of light. He uses it to escape pursuit and fly through walls, but also to enter a human's body and attempt possession, successfully with Gaius.
Bar Brawl: A Medieval bar brawl at the beginning of 3x04.
Bar Slide: When Gwaine first appears in 3x08, he's being slid across the bar.
Bastard Bastard: Morgana. She is the illegitimate daughter of Uther and Vivienne.
Battle of Wits: Often between arch enemies Merlin and Morgana, who are the two most powerful characters in the series. Before Arthur and Gwen become King and Queen, Merlin was the one person who prevented Morgana from completely destroying Camelot.
Beautiful Dreamer: Almost every character has watched either Merlin or Guinevere sleep at one stage or another. The most notable examples are when Merlin lends Gwen his bed in To Kill The King and then stays by her as she sleeps, and when Arthur finds Gwen under a sleeping spell in The Fires of Idirsholas he watches her for a few moments after putting her on Morgana's bed.
Beauty Is Bad: With few exceptions Freya, Mithian, every single beautiful woman on the show ends up being a villain, or is at least meant to be perceived as unsympathetic.
Subverted marvellously with Princess Mithian. You'd think they would have made her as unpleasant as possible so Arthur would come and throw himself at Gwen again but she's actually rather nice.
Beleaguered Assistant: Several times Merlin had to help bail Arthur out of some sticky situations. Particularly in the episode The Gates Of Avalon, where poor Merlin had to deal with the consequences of a spellbound Arthur courting Sophia. In this one episode alone, Merlin got placed in the stocks three times!
Berserk Button: Even if you are an incredibly powerful sorceress, do not try to kill Gaius with magic in front of Merlin. Of the two who have tried so far, one was telekinetically hurled into a pillar at neck-breaking speed, and the other was struck in the face by lightning.
It is generally considered a bad idea to harm Morgause in front of Morgana. She doesn't like it. At all.
Mess with a certain maid-servant and you'll have to deal with her best friend (a powerful warlock), her boyfriend (the crown prince), and a team of the best knights in the land. Best to just leave her be...
A seemingly all-powerful Future Merlin, standing triumphant over her on the field of battle, a staff in hand and a look of utter Tranquil Fury, literally becomes the stuff of nightmares to Morgana in Series 4.
Morgana: Help me, Emrys! Please!
Merlin: Is this really what you wanted, Morgana?!
Morgana, herself. She was once one of the nicest characters on the show, but even then demonstrated she could be a dangerous adversary. Unfortunately, she became not so nice later on.
Beware the Quiet Ones: Mordred. When Mordred was a child, he didn't talk much, if ever. But he smashed a mirror with his powers when he was angry and upset over one of his kind being executed. That was a clear sign to not mess with this kid.
Big Bad Ensemble: Morgana was paired up with a different cohort once per season; first with Morgause, then Agravaine, and at the very end with Mordred. Then there were the Monsters of the Week, who were usually out to seek revenge against King Uther, who was himself something of a villain.
Big Brother Instinct: Kilgharrah's treatment of Merlin in Series 2 is best described as a come and go fondness. In Series 3, after becoming spiritual brothers, Kilgharrah burns up Serkets trying to kill Merlin, doesn't want him to leave the cave until he's fully recovered, and allows him to ride him despite the fact that the series 3 finale shows he detests being used as a horse. He still occasionally treats him like an idiot, but given that we have only one talking dragon to draw references from, this could have been a normal big brother relationship among dragons.
Arthur and the knights of the Round Table, especially Gwaine and Lancelot, are fiercely protective of Merlin. Justified in that he physically looks small, fragile and scrawny and is also a few years younger than all of them, but still funny considering he could kill all of them easily with just a wave of his hand.
Arthur, after barely knowing Mordred a few weeks, is already showering him with attention, praising him and going to insane lengths to save his life - lampshaded by Merlin and Gwen. "The Disir" ends with an adorable moment of them sword-fighting and then Arthur lifting Mordred up in the air, goofing off like a big brother with his little brother. It's oddly fitting, considering in the myths Mordred was supposed to be Arthur's son.
Merlin also had this towards young!Mordred, Daegal and Gilli.
Big Brother Mentor: Arthur probably fancies himself as this to Merlin, though Gwaine or Lancelot probably fit the bill better.
Arthur ends being one for Mordred. Gwen points out he's growing fond of the boy, and Arthur couldn't shut up on what a promising knight Mordred is.
Big Damn Heroes: Merlin and Arthur, usually. Occasionally Morgana, Gwen, Gaius and Lancelot.
Every good character in The Coming Of Arthur Part Two.
The Big Damn Kiss: Arthur and Gwen's first kiss came complete with dramatic lighting and an orchestra of violins.
Heck, it's more noteworthy when one of their kisses isn't a Big Damn Kiss.
Big Entrance: Morgause and Mithian both get fairly impressive entrances onto the show. Tristan de Bois as well when he interrupts Arthur's crowning ceremony by leaping through a stained glass window on horseback.
Big "NO!": When Gaius dies for Merlin and Merlin rushes to his side only to find him dead already, Merlin says "Nnnnnnoooooo!" twice. Except that Gaius wasn't actually dead.
Morgana lets out an absolutely humongous one when Morgause is apparently killed; seriously, we're not kidding, it LITERALLY brings the roof down. Literally.
Big Screwed-Up Family: As of the end of series three, the Pendragons definitely qualify, what with Uther and Arthur's strained relationship and the fact that Morgana is not only Uther's illegitimate daughter and Arthur's unacknowledged half-sister, but actively trying to kill them both. Both of Arthurs uncles tried to avenge Ygraine’s death: Tristan by coming back from the grave to kill Uther and Agravaine by plotting with Morgana.
Billing Displacement: Angel Coulby is credited before Bradley James in the opening credits; a little strange considering Arthur is the show's Deuteragonist. Speculation is that Angel went first because she was the most established cast member at the inception of the show, or that the names are simply in alphabetic order after Colin Morgan.
In the episode Another's Sorrow James Fox is ranked before Janet Montgomery, even though Montgomery is in nearly every scene of the episode and Fox's role barely constitutes a cameo.
Bit Character: Geoffrey of Monmouth, who started out as the court genealogist, but who now also serves as Mr. Exposition whenever Gaius isn't around, and is trotted out whenever the writers need someone to preside over a coronation or wedding. He even seems to be a member of the council, and is the one who backs up Guinevere in The Darkest Hour.
Also Audrey, the head cook of Camelot's castle kitchens, and Isildur, a druid leader. Both have appeared in three episodes each.
Bittersweet Ending: The end of series three. Though the Knights of the Round Table and Guinevere return to Camelot in triumph, the hug that Arthur and Guinevere share is clearly marked by their sadness over Morgana, and Merlin's smile fades as he watches them, no doubt reminded of Freya.
The entire series pretty much ends like this, Morgana has finally been defeated for good and Camelot is safe, but Arthur was killed in the process along with Gwaine. In addition, the epilogue shows that everybody Merlin once knew is now dead. Nevertheless, the fact that Merlin is still alive means he's waiting for the day when Arthur will rise again at the day of Albion's greatest need.
Its worse when you think about it. The Golden Age may never have come to pass since Arthur was supposed to bring it about. Albion is not united so other kings may invade thinking Gwen weak. The Saxons are still a threat. Gaius can only have a few years left. Magic users would still hate Camelot. Merlin is no longer around to help protect Camelot. Arthur's whole return may have been made up by The Great Dragon to comfort Merlin or he might have been wrong. He was wrong on other things.
Black and Grey Morality: Uther hunts down anyone related to magic, even healers, even children. He's a cruel dictator. Getting rid of him would be a good thing. However the villains trying to kill him, Morgana and Morgause, have some evil tendencies in a Well-Intentioned Extremist way. They will kill others, but only if they have to to get to Uther or Arthur later.
Black Magic: Morgana, Morgause, Nimueh and Mordred all practice Dark Magic.
Bling of War: Morgana's "action gear" involves a shiny metal corset of some kind. Unless she were shot directly in the stomach, it's utterly impractical.
Bloodless Carnage: Plenty of people die in this series, but you will rarely see any of them actually bleed.
Bluff the Impostor: Arthur does this to goblin-possessed Gaius - he talks casually about Merlin's uselessness and impending death sentence, and when "Gaius" isn't bothered, Arthur knows something's up.
And Merlin and Arthur bond over one of them having a missing father and the other a missing mother.
Book Ends: In the first episode of series two Guinevere saves Arthur's life from a flying gargoyle in the castle courtyard by tackling him to the ground. In the last episode of series two Arthur saves Guinevere's life from a flying dragon in the castle courtyard by tackling her to the ground.
In the first episode of series three Merlin is witness to a hug between Arthur and Morgana; in the last episode he watches a similar embrace between Arthur and Guinevere.
In both the opening and the closing two-parters of Series 3 Camelot was attacked by an army of immortal soldiers sent by Morgause and Cenred.
Arthur is crowned King at the beginning of series 4; Guinevere is crowned Queen at its conclusion.
The beginning of Series 1 sees Merlin walking on a road to Camelot; the end of Series 5 sees older!Merlin walking on a road in the same manner, waiting for Arthur.
Bookworm: Merlin. He is always reading and researching a lot.
Brainwashed: This happens to Arthur in at least three episodes, with the first case bordering near Brainwashed and Crazy. In the third case, it's by Merlin. Then it happens with Gwen in season 5.
Brainwashed and Crazy: In A Servant of Two Masters in series 4, Merlin is bewitched by Morgana to kill Arthur, but is thankfully a terrible assassin.
The knights in "Lamia". They start fighting each other, being incredibly disrespectful to Merlin (to whom they're usually Cool Big Brothers, and threatening Merlin and Gwen for speaking out.
In season five, Morgana is at it again, this time with Gwen.
Break the Cutie: Morgana. Goes through a season of terror only to have the one person in Camelot she could trust poison her. Ouch. Not to mention being trapped in a pit for about two years straight. With a growing dragon. And in chains.
Averted by Merlin, thanks to being an Iron Woobie. But let's face it, half the reason he hasn't gone into total breakdown is because of his potential to be a terrifying Woobie, Destroyer of Worlds if he did.
Guinevere in Lancelot du Lac, in which she is enchanted into betraying Arthur by Morgana, is banished from Camelot and none of her friends are there to see her off except Merlin. Not even her own brother wants to see her. The cherry on top? Only the audience and the villains know she was enchanted, so she believes everything is her fault. This isn't so much Break the Cutie as smash her to bits, stomp on the pieces, and grind them to dust. As if that isn't enough, she gets enchanted AGAIN by Morgana to kill Arthur and was probably tormented a bit while she was held captive.
Aithusa. Being trapped in a pit you outgrow and end up barely able to even move in at all will do that to you.
Bullying a Dragon: Quite literally, in one case. Metaphorically, it often happens elsewhere. Merlin tries to play this in the first episode by warning Arthur he doesn't want to see what he's capable of. But since he can't use his magic in public, it was a pretty futile threat, and Merlin just ends up getting his ass kicked.
Although in the literal example, said dragon does take a shot at incinerating Merlin, and Merlin magically blocks the fire.
Butt Monkey: Merlin, especially when "helping" Arthur with his training exercises.
Morgana Pendragon as well. Even before her Heel-Face Turn, the writers did not seem to like her.
Call Back: In the pilot episode Merlin says of Arthur: "I said you were a prat, I just didn't know you were a royal one." In the final episode of the first series, on saying goodbye to Arthur, they have the following exchange:
Arthur:You know, sometimes I don't think you know who I am.
Merlin:Oh, I know who you are. You're a prat. And a royal one.
Arthur and Gwen's conversation at the end of 3X10 is filled with allusions to the one they had at the conclusion of 2X02; particularly repetition of the words: "when you/I am King, things will be different."
In 2x04, Merlin tells Arthur that everyone can see his feelings for Gwen and that even a "blind man could see it." Morgana repeats a similar line to Arthur in 3x10.
Merlin giving Morgana flowers in 2x03 and later in a deleted scene in 3x01.
Merlin's conversation with Morgana in 3x07:
Morgana: Why are you telling me this?
Merlin: Because I don't understand why anyone would want to hurt their friends.
Morgana: No, you just poison them.
In 1x13, Morgana pulls Merlin behind a pillar to warn him about Arthur being in danger. In 3x02, Morgana pulls Merlin behind a pillar once more, but only to threaten him not expose her villainy by reminding that Uther would have him executed if she revealed to him that Merlin poisoned her.
In 2x12, Morgana recalls to Morgause her assassination attempt on Uther in 1x12.
Merlin and Arthur's conversation on horse in 4x01 alludes to 2x01:
Arthur: Yes, that you're a clotpole.
Merlin: That's my word.
In 4x05, Queen Annis says with almost reluctant admiration "There is something about you, Arthur Pendragon..." which seems very reminiscent of something Arthur himself to Merlin in 1x01.
On the same note, Arthur's line in 1x01 was "There's something about you, Merlin." Perhaps coincidentally, Gwen delivers the exact same line to Merlin in 4x08.
The scene where Gwen sentences her servant to death mirrors the scene where Gwen is dragged before Uther.
At the end of 3x02, Uther presents Morgana to the court as the person who turned the tide of the battle and saved Camelot, causing everyone present to applaud her bravery. Morgana was, of course, the traitor who initiated the whole thing. Episode 5x07 ends with Arthur congratulating Gwen for rooting out the traitor who had been trying to kill him (she was, of course, the traitor.) The episode ends with the court cheering "Long live the Queen!"
In 2x13, Arthur advises Merlin with "No man is worth your tears", to which Merlin replies "You're certainly not". In the Grand Finale, Merlin breaks down when Arthur is dying and Arthur tries to calm him.
Cardboard Prison: Not only Camelot's dungeons, but also its "impregnable" vaults.
Cassandra Truth: Merlin lives this trope. In every season and most episodes therein, Merlin usually has foreknowledge of the (dis)loyalties of basically everyone. But he can't ever prove this because it variously involves a) exposing himself as a wizard, b) selling out someone he would rather not, or c) being pitted against someone who Uther and/or Arthur trust implicitly. You would think, considering everything Merlin says turns out to be true, people might just start giving him the benefit of the doubt.
More conventionally, there's one instance of Merlin bursting into the throne room and insisting he's a wizard.
Surprisingly, Arthur finally catches on to this in the season 4 finale. He realizes that Merlin knew, and has always known, about such betrayals. Arthur, meanwhile, always sees the best in people right up until they stab him in the back. He finds it quite frustrating that the people he treats as friends are so willing to betray him. He predictably reacts quite badly to Merlin's confession of having magic at first.
Also obviously Morgana due to her powers as a seer which ultimately are often ignored especially by Arthur who frequently dismisses them as nightmares or taking it as a sign of romantic attraction that she dreams about him (this is entirely shippers choice although it does seem to be rather obvious in season 1!) This is subverted by the fact that Gauis and Merlin often use these dreams to their own advantage to help Merlin protect Arthur-often without telling her and again almost always attempting to brush it off as just a dream
Cast Full of Pretty Boys: King Arthur and all of the Knights at The Round Table are all resident Hunk's. It also helps that the titular character (Merlin himself) of the series is a real Pretty Boy.
Catapult Nightmare: Despite suffering from at least one nightmare per episode, Morgana has surprisingly few of these. However, most recently she flung herself upright from a dream about Gwen becoming Queen of Camelot. She later does this when Agravaine bursts into her hut in Series 4, though, she's not waking from a nightmare, she's just scared.
In The Last Dragonlord, Balinor refuses to help Camelot initially due to his legitimate grudge against Uther, but changes his mind.
Changeling Tale: Unsurprisingly, "The Changeling", even though they tweak the traditional definition of what a changeling is.
Character Title: Merlin, obviously, but also episodes themselves such as Lancelot and Gwaine.
Characterization Marches On: Before becoming something of a regular in the third series, Ensemble Dark Horse Sir Leon had a few scenes in the second. One of his first appearances involves him violently tearing apart Gaius's study in the search for evidence of magic. The sight of him smashing bottles and ripping down tapestries is completely at odds with the gentler character of later episodes, who is also on good enough terms with Gaius (in a Deleted Scene) to confide in him that the knights have no confidence in Uther's ability to rule.
Chekhov's Gunman: The fact that Freya was cremated on the waters of the same lake that Merlin threw Excalibur into seems mightily suggestive.
In "The Coming Of Arthur Part 2" she is pretty much confirmed to be the Lady of the Lake.
Chickification: Gwen in series two, later in season three she's regaining her reputation as a Badass Normal (fending off an intruder with a poker, joining the men on their rescue mission, lighting a fire when Arthur cannot), whilst still remaining within the boundaries of what a slight young woman would realistically be capable of.
Gwen: I am the blacksmith's daughter, remember?
But still reverts to "Stay in the Kitchen and make bandages" for the series finale, and whilst season four has her defending Merlin from an enemy and having a sword fight with Morgana, season five has her playing this trope fully.
The Chick: Gwen. She is the female centrepiece of the series.
Children Are Innocent: Initially played straight with Mordred, who despite being supposedly destined for evil, is at first just an ordinary (if telepathic) little boy. His morality becomes more and more ambiguous with each subsequent appearance, as Uther's persecution drives him to become more and more vengeful. Although he is defending himself against adults, it's still pretty scary for a kid who was raised by an extremely pacifistic people to kill without remorse.
The Chosen Zero: Merlin's immediate reaction to being told that Arthur is the destined King who will save the land is "There must be another Arthur, because this one's an idiot!"
Clap Your Hands If You Believe: When Arthur is trying to draw Excalibur, Merlin says that he needs to truly believe he can in order to do it. Subverted since Merlin was just trying to boost Arthur's confidence: once Arthur is sold on Merlin's story, Merlin covertly uses magic to make the task extremely easy for Arthur, thus reinforcing the idea he was trying to instill.
Closet Shuffle: In Camelot, cabinets are not meant for storage. They're meant as convenient hiding places for Merlin.
Clothing Damage: Nimueh must have been dragged through a hedge at some point as the bottom half of her dress is ripped in a way that exposes Michelle Ryan's legs. Well, she has been living in a cave for twenty years!
Also Freya's dress, but it can be explained since she's been Halig's prisoner for who-knows-how-long.
Colour-Coded for Your Convenience: Merlin and Arthur usually wear blue and red respectively, as a near-literal example of Red Oni, Blue Oni. Spirited Young Lady and Rebellious Princess Morgana wears bright, jewel-like colours such as reds, blues, purples, and greens, whilst the gentler Shrinking Violet Guinevere wears almost every shade of pastel imaginable: lavender, peach, pink, and light blue. By series four, the bad guys (Morgana, Agravaine, Helios, and Shade!Lancelot) wear black, whilst those with magical powers are usually delinated by the colour green, particularly Mordred and the other Druids, who wear green cloaks.
Crystal Ball: Not "balls", but there have been at least three examples of crystals that show the future: Morgause's crystal, the Crystal of Neahtid, and the Crystal Cave.
Arthur: You can't leave him here [on the floor]! We have to get him onto the bed.
Merlin: Why? He's asleep. He's not going to know.
Merlin: Alright, I'll get him a pillow.
Arthur: He's the king!
Merlin: You're right....two pillows!
Composite Object: As with many modern retellings, Excalibur is combined with the Sword in the Stone (the oldest versions of the tale describe them as two very distinct swords - when Arthur breaks the latter in battle, he gains the former from the Lady of the Lake).
Conflicting Loyalty: Merlin, most especially in series 2. His destiny is clearly to stand by Arthur, but Arthur's views on magic, even if only impressed upon him by Uther, can make for some not inconsiderable moral tension. The Sins of The Father showcases this dilemma to particularly heart-breaking effect.
Morgana to some degree as well regarding Uther and his ruthlessness towards magic. Made all the worse when she finds out that she's a seer and has magic herself
Arthur also has moments where he butts heads with Uther, usually when the latter is being too harsh, accusing an obviously innocent person of witchcraft, or not taking good enough care of the people of Camelot.
Costume Porn: Morgana's entire wardrobe, including dresses that wouldn't look too out of place at a cocktail party, as well as the gowns of various ladies and princesses that turn up throughout the series and Guinevere's coronation gown◊. The decoration on Arthur's armor◊ is remarkably intricate although it won't show unless in close-up.
Cradling Your Kill: Merlin with Morgana's body in 2x12. He also holds Morgana as she's dying in the series finale.
Merlin can be this at times as well. He demonstrates jealousy toward anyone who poses a threat to his relationship with Arthur, such as Cedric and Princess Mithian, and is willing to share Arthur with only one other person in the world: Guinevere, who happens to be his own very close friend.
Crazy-Prepared: Myror just happened to be carrying a retractable, needle-tipped lance along with him.
If the spell translations are to be believed (hinges on Word of God here), Merlin is too. Half the spells are so tailored to the situation that either he's making them up as he goes or he really does learn spells just in case he wants a magnetic sword, he needs to drop bed covers on someone, or he needs to throw a bench.
Creepy Child: Mordred. Also, a hallucination Uther suffers at the beginning of Series 3.
The ghost child from A Herald of a New Age that possesses Elyan.
Cut His Heart Out with a Spoon: Non-lethal version. In "The Death Song of Uther Pendragon", Arthur warns Merlin to keep quiet about the spirit-summoning horn he intends to use. Merlin points out that Arthur is making said threat while holding a spoon. Cut to outside the room, and Merlin suddenly shouts in pain.