While there were plenty of running gags on Merlin, one of the best was how oblivious Arthur was to Merlin's magic. Considering that he spent the most time with the eponymous sorcerer, it was quite hilarious that he didn't seem to realize that Merlin was one of the most powerful beings in the world.
What made the situation even funnier was the fact that other people, including minor characters and villains, were quickly able to pick up on Merlin's talents since he wasn't particularly careful in hiding them. Although Arthur did eventually find out in the show's last episode, he could have easily found out earlier if some of these characters decided to expose the wizard.
Update November 05, 2021: It may have been nearly ten years since Arthur sadly died in Merlin, but it appears the Once and Future King's presence is still around as his stories have influenced many movies. From King Arthur: Legend of the Sword to The Green Knight, viewers have enjoyed seeing Arthur's Camelot flourish as he has forged alliances with an array of sorcerers (including Merlin and Morgana). But could the same results have occurred if the BBC's adaptation followed down the same path? Considering how Arthur reacted to Merlin's powers, he and Merlin would have created the greatest kingdom of all.
Gaius (S1 Ep1)
The uncle and surrogate father of Merlin, Gaius played an important part in the young magician's life from the very beginning. After the pair met in "The Dragon's Call," Gaius first saw Merlin use his magic when he saved him from a dangerous and possible fatal fall. Although Merlin denied using magic, he once again exposed his magic when Gaius tricked him into preventing a bucket of water from spilling off the table.
In the many years that followed, Gaius spent years protecting Merlin's secret - going as far as to put his life on the line for him. He also spent many of those years teaching Merlin how to hone his skills and defeat several powerful foes. Fans adored watching this duo as they always concocted some interesting and hilarious schemes.
Kilgharrah (S1 Ep1)
While Merlin certainly had a strong team behind him that helped him save the day, there was one thing that was usually the brains behind the operation: Kilgharrah. First appearing in "The Dragon's Call," Merlin was surprised to find The Great Dragon hidden beneath the castle and that he knew practically everything about him. It was Kilgharrah who also told Merlin about his great destiny.
Although Kilgharrah and Merlin didn't always see eye to eye, he did play an important part in Merlin's arc. He would often provide Merlin with some wise advice and knowledge about the magical foes he faced. Merlin and Camelot wouldn't have got as far as he did without his help.
Nimueh (S1 Ep3)
There have been plenty of iconic villains in Merlin, but one that proved to be quite memorable was Nimueh, a High Priestess of the Old Religion. While Camelot suffered a lot as a result of her plans, the viewers soon discovered that Nimueh only wanted revenge against Uther after he blamed her for his wife's death and killed all of her friends.
However, she soon realized this would not be as easy as she thought as "The Mark of Nimueh" saw her discover Merlin's powers. Sadly, the viewers only got to witness them have an all-out battle once since Merlin killed her in the last episode of the season. Considering the extent of her powers, it would have been great if the writers had partnered Nimueh with Morgana or found a scene where she and Merlin formed a brief alliance.
Lancelot (S1 Ep5)
Known to be the bravest and most noble knight of all, Lancelot was the only Knight of the Round Table to ever discover Merlin's powers. He first discovered Merlin's magic in "Lancelot" when he witnessed Merlin use an enchantment on his lance, helping him to defeat the Griffin.
Instead of turning him in, Lancelot surprised everyone when he promised to keep Merlin's secret (and he did so until the day he died). It really was a shame that Lancelot was in a limited number of episodes as he was one of the few people who really appreciated Merlin for who he was and genuinely cared about his well-being. Fans would have loved to have seen them pair up on more adventures before Lancelot's untimely death.
Edwin Muirden (S1 Ep6)
Edwin Muirden was a warlock who wanted to avenge his parents' deaths at the hands of Uther. He posed as a physician and claimed he could heal Morgana ("A Remedy to Cure All Ills"). While there had been plenty of iconic villains over the years, Edwin was one of the most intriguing ones. He quickly got Uther on his side and even managed to convince the court to turn on Gaius.
Eventually, Edwin realized that Merlin had magic when he saw him open a box that had been sealed with a spell. Edwin then used this knowledge to blackmail Gaius while also hoping to gain Merlin's allegiance. This was a storyline that could have certainly played out across the series.
Mordred (S1 Ep8)
Although it's not known exactly how Mordred knew about Merlin's real identity, the first time Merlin discovers they have a magical bond is in "The Beginning Of The End" when a young Mordred telepathically called out to him for help.
While Merlin and Mordred didn't exactly have the easiest of relationships, especially since Merlin didn't trust him as he had been warned that Mordred would kill Arthur, Mordred did keep his secret for many years. It did disappoint fans that Merlin's concern with the prophecy got in the way of them building a friendship, as Merlin could have become somewhat of a big brother to Mordred and mentored him in their craft. Sadly, this was not the case and Mordred died after committing several devastating betrayals.
Hunith (S1 Ep10)
Considering that Hunith was Merlin's mother and had a relationship with Balinor, it's obvious that she knew of her son's magic from an early age. However, as Merlin's powers continued to grow, Hunith revealed in a letter that she thought it was best to send him to Gaius in the hopes that he could give Merlin guidance and purpose ("The Dragon Call").
While Hunith only appeared in three episodes, the viewers learned a lot about her relationship with Merlin and Gaius. They could see that she was fiercely loyal and would do anything she could to keep them out of harm's way. She also had a pure and selfless heart too, which allowed viewers to see why Merlin always strived to bring out the good in everyone.
Will (S1 Ep10)
Will was Merlin's childhood friend from Ealdor and the only person, aside from Hunith, who knew of Merlin's powers. The viewers first met him in "The Moment of Truth" when Merlin returns to his village to help him and the other residents protect their home from Kanen's men. Sadly, Will ended up dying in the battle after he saved Arthur.
Although Will made one appearance, fans could tell that he was a great friend to Merlin. He had every opportunity to expose Merlin but didn't because he knew of the good Merlin could do. The fact that Will's last moments also involved protecting Merlin showed that he would always have his friend's back.
Cornelius Sigan (S2 Ep1)
Introduced in "The Curse of Cornelius Sigan," the viewers met Cornelius Sigan as he inhabited the body of the thief, Cedric, who robbed his grave. After he witnesses Merlin perform magic to protect Arthur, he offers to form an alliance with him. However, he proved that he couldn't be trusted when he tried to possess Merlin's body after realizing he was more powerful than him.
Considering that Cornelius was meant to be one of the most powerful sorcerers in the world, it was a little disappointing and anti-climatic that they didn't have a major showdown. Instead, he was just forgotten about and sealed back in the vaults of Camelot. Morgana could have easily used him as an ally and she certainly would have discovered Merlin's identity quicker.
Jonas (S2 Ep5)
The right-hand man of Lady Catrina, Jonas also made his introduction in the season 2 episode "Beauty and the Beast," where he helped her trick Uther into marrying her. Jonas was the first person to discover Merlin's powers as he watched him try to use an enchantment on Lady Catrina.
Jonas was a lot more intelligent than Lady Catrina as he realized the danger they were in when witnessing Merlin's powers. It's also likely that he was the one who organized the plan for her to marry Uther since he was the one that arranged her potions. The only issue was that he didn't seem to realize what exposing Merlin could have done for him or Lady Catrina.
Lady Catrina (S2 Ep5)
Arguably one of the funniest and best villains to ever appear on Merlin, Lady Catrina managed to make fans laugh when she tricked Uther into marrying her ("Beauty and the Beast"). However, that didn't mean there were those who didn't approve of the match. Since Merlin was the first person to discover that she was a troll, she had a tough time executing her plan.
She eventually discovered his powers when she felt someone using magic to transform her back into a troll. Catrina could have easily turned Merlin over once she realized what he did. However, given that she was a troll and was just interested in increasing her wealth, she didn't seem intelligent enough to realize that getting rid of Merlin would have benefitted her more.
Freya (S2 Ep9)
In "The Lady of The Lake," fans were introduced to a cursed and hunted druid named Freya. Since Merlin couldn't stand the thought of her being executed at the hands of Uther, he saved her from a bounty hunter and tried his best to keep her safe. They two eventually grew close, with Merlin using his magic freely around her and also coming up with a plan so they could run away together. Unfortunately, this did not end well as Freya ended up dying in his arms.
For many fans, Freya and Merlin's romance was quite endearing. The viewers could see that the two genuinely enjoyed each other's company and could have had lived a happy life together if it wasn't for their destinies. It's such a shame that she died because Freya was just as refreshing as the Merlin characters fans met in season 1.
Balinor (S2 Ep13)
In "The Last Dragonlord," Merlin is seen to meet his father for the first time. Although Balinor did treat them with hostility upon first meeting them, mainly due to the fact that Uther had tried to have him killed previously, he began to warm up to Merlin once he discovered his identity.
Since he was the last Dragonlord at this point in time, Balinor would have known instantly that his son had magic capabilities. Sadly, the viewers didn't get to see them bond for much longer as Balinor died while saving Merlin. They may not have known each other for long but Balinor did end up changing Merlin's life since he had now inherited his father's powers (which then led to a range of interesting storylines).
The Goblin (S3 Ep3)
Appearing in the episode "Goblin's Gold," the Goblin was a minor character that surprisingly almost brought Camelot to its knees. The creature eventually discovered Merlin's powers after the young sorcerer used his magic to stop him from leaving his chambers.
Surprisingly, it was the Goblin that almost succeeded in killing Merlin after he went straight to Uther and confessed that Merlin was a sorcerer. He also proved to be quite intelligent as he used Gaius' body to ensure nobody would hurt him. It wasn't meant to be taken seriously but that might have been the writers' way of suggesting no one should underestimate any character involved.
Taliesin (S3 Ep5)
“Taliesin was a Seer to the Great Kings of old. It is said that the Crystal Cave was the source of his prophecies.” Taliesin appeared to Merlin in the Valley of the Fallen Kings at a time where Merlin was feeling hopeless ("The Crystal Cave"). He healed an unconscious and injured Arthur after Merlin found he could not do it.
Given that Taliesin was a Seer, he would have already known that Merlin was Emrys and what his future entailed. However, like many of the other magical beings in the show, he only got involved when it was required. He didn't really have much impact on the narrative so fans felt indifferent when he didn't make another appearance on the show again.
Grunhilda (S3 Ep6)
Introduced in the season 3 episode "The Changeling," Gruhilda made quite an impression on the fans as she wasn't the ordinary villain everyone was used to. Rather, Gruhilda was actually funny and likable. She just seemed to be on the wrong side of the battle in this one.
After discovering that Gruhilda was a faerie, Merlin used his magic on her to trap her in the cellars of Camelot. Gruhilda seemed unaware of Merlin's reputation and wasn't concerned either by the fact that he was a sorcerer. Since she was also so consumed with her anger, Gruhilda made a reckless decision to attack Merlin without protecting herself (ultimately leading to her death).
Grettir (S3 Ep8)
Introduced in the episode "The Eye of The Phoenix," Grettir was the helpful sorcerer who guarded the bridge that gave passage to the Fisher King's Perilous Lands. He greeted Arthur as "Courage" but told him that he would also need "Strength" and "Magic" to complete the quest.
Later on, the viewers discover that Grettir was referring to Gwaine and Merlin as he calls Merlin "Magic" when they first meet. Like many other magic users, Grettir probably learned about Merlin's power when the prophecy was created. He also wanted magic to be restored to the land, which is why he didn't expose Merlin's identity (although it was a bit mischievous of him to hint at it by code).
Fisher King (S3 Ep8)
The Fisher King was a sorcerer who had been waiting for death. When Merlin found him in the Perilous Lands, the Fish King knew he was Emrys, having foreseen him ("The Eye of The Phoenix"). He gave him a vial of water from the Lake of Avalon and in return received the Phoenix Eye, freeing him from his current state.
Compared to all the other minor characters, The Fisher King played an important part in Merlin's arc. By providing him with a vial of water from Avalon, he provided him with the knowledge of how to defeat Morgause's army. He basically gave Merlin and Arthur the hope they had desperately needed all along.
Gilli (S3 Ep11)
First seen in "The Sorcerer's Shadow," Gilli is a young sorcerer like Merlin, except he uses his powers without caution. He uses his powers to increase his chances in the Decennial Tournament in Camelot. Gilli makes acquaintance with Merlin after saving him with magic.
When Gilli reaches the final round of the tournament against Uther, Merlin reveals his magic to Gilli in an attempt to make him understand that he is not alone and he knows how Gilli feels. Luckily, his words get through to Gilli and he leaves soon after without anyone being harmed. Although the viewers didn't see him again they would have liked to have been given an update on his whereabouts after.
Iseldir (S3 Ep12)
Iseldir was introduced in season 1 as one of the chieftains of the druid clan. However, Merlin officially meets Iseldir two seasons later in "The Coming Of Arthur: Part 1" when he addresses him by his sorcerer's name and told him to protect the Cup of Life (via telepathically).
While it's not completely explained as to how Iseldir knew of Merlin's identity, some believe that he might have learned about it through magic itself or the druid community. Nevertheless, despite them hardly interacting, Iseldir proved to be a loyal ally to Merlin, helping him show Arthur all of the good that magic could be used for.