One of the great Merlin fanfictions is 'The Once and Future Queen'. It presents an interesting take on Arthur and Merlin's relationship in a more complex way. Another is 'A Different Destiny' which rewrites the fates of the characters in a creative and engaging manner. And 'Merlin's Hidden Powers' explores Merlin's magic in depth and shows how it could have been used in different scenarios.
There are quite a few excellent Merlin fanfictions. For example, 'The Sorcerer's Apprentice Redux' is a wonderful one. It reimagines Merlin's early days as an apprentice in a more detailed and adventurous way. It really captures the essence of his character growth. Another great piece is 'Arthur and Merlin: A New Era' which speculates on what could have happened if Arthur had known about Merlin's magic from the start. This fanfiction is full of emotional moments and great character interactions. Also, 'The Magic Within the Court' shows how Merlin's magic could have influenced the politics and daily life within Camelot in a very intriguing way.
Well, 'The Bond Beyond Magic' is a top Merlin fanfiction. It delves into the deep friendship between Merlin and Arthur, showing how their bond transcends not just the magical aspects but also the social differences in Camelot. Then there's 'Merlin's True Calling' which focuses on Merlin's journey to fully understand and accept his role as a powerful wizard. 'The Enchanted Camelot' is also great as it adds new magical elements to the world of Camelot and gives the characters new challenges to face.