One great Merlin - Supernatural crossover fanfic is 'The Hunter and the Warlock'. It combines the magic of Merlin's world with the demon - hunting aspect of Supernatural in a really interesting way. The characters from both shows interact in a believable manner, making for an exciting read.
There's also 'Magic and Monsters'. This fic has a unique take on how the Supernatural universe would react to Merlin's brand of magic. It shows how the characters from Supernatural might view Merlin as both a powerful ally and a potential threat, with a lot of character development along the way.
A popular one is 'When Two Worlds Collide'. In this fanfiction, the Winchesters end up in Camelot. It's full of action as they try to figure out how to get back home while also dealing with Merlin's enemies. The way the author blends the different mythologies and power systems of both shows is quite engaging.
I really like 'Crossroads of Krypton and the Hunting Life'. In this fanfiction, the writers did an amazing job of bringing in the mythology of Smallville and Supernatural. Dean and Sam Winchester end up in Smallville and get involved with Clark's world. It's full of action and some really cool character moments. It shows how the different powers and skills of the characters from both shows can work together or clash in interesting situations.
One great Supernatural and NCIS crossover fanfiction is 'The Hunt in Quantico'. It combines the mystery-solving aspect of NCIS with the supernatural elements of Supernatural really well. The characters from both shows interact in a very believable way, and the plot keeps you on the edge of your seat.
A popular one is 'Crossing Paths'. This fanfiction has an interesting take on the crossover. It starts with a mystery that involves both the Supernatural and Buffy universes. The author does a great job of writing the characters true to their original personalities. Buffy's determination and the Winchesters' tough - guy attitudes are on full display, and the story builds up to a very satisfying climax.
One great 'Supernatural' and 'Arrow' crossover fanfiction is 'The Hunt in Starling City'. It combines the dark, supernatural elements of 'Supernatural' with the gritty, urban setting of 'Arrow'. The story has Dean and Sam Winchester arriving in Starling City to hunt a demon that's been causing chaos in the criminal underworld, which draws the attention of Oliver Queen and his team. They initially clash but then realize they need to work together to stop the greater evil.
Well, there's 'Parallel Encounters'. In this fanfic, the settings of Supernatural and Tramiplier are merged in a really interesting way. It starts with a character from Tramiplier accidentally stumbling into the world of Supernatural. The story then unfolds as they try to find their way back while getting involved in the ongoing battles against demons and other evils in the Supernatural realm. It's full of action and some really cool character interactions.
Themes of destiny and free will also play a big part. In both shows, the characters struggle with their fates. In a crossover, they can compare notes on how they've dealt with prophecies and whether they believe they can change their destinies. For instance, Merlin was prophesied to bring about great change, and the Winchesters have often been part of prophecies in their own world.
One great 'Merlin and Harry Potter' crossover fanfic is 'The Merlin Effect in Hogwarts'. It combines the magic systems of both universes really well. The characters from Merlin, like Merlin himself, fit surprisingly well into the Hogwarts setting. They interact with Harry and his friends in interesting ways, for example, Merlin uses his unique magic to solve some of the problems at Hogwarts that the students there are facing. It's a fun read for fans of both series.
A popular one is 'Merlin and the Kingsman Trainee'. In this fanfiction, Merlin takes on a trainee who has a lot to learn. It's interesting because it delves into Merlin's teaching style and how he imparts his wisdom and skills. There are some great character interactions and a bit of humor thrown in as well.
One great 'Merlin and Escanor' fanfiction is 'The Bond Beyond Kingdoms'. It beautifully explores their relationship in a world where they have to team up against a common magical threat. The story delves deep into their individual powers and how they complement each other.
One great 'Merlin and Emma' fanfiction is 'The Enchanted Bond'. It beautifully weaves their two different magical worlds together. The story has an interesting plot where Merlin uses his ancient magic to help Emma with her modern - day magic problems in Storybrooke. It's a great read for fans who love to see crossovers.