One great 'Fate Stay Night Merlin Fanfiction' is 'Merlin's True Role'. It delves into Merlin's backstory and how his magic could have influenced the events of the Holy Grail War in ways not shown in the original. It has a really interesting take on his relationship with the other servants as well.
Merlin is obviously one of the main characters. He is a powerful wizard with great influence. Then there's probably Arthur, as it is related to Arthurian legend. There might also be other knights or magical beings that play important roles in the story.
One interesting Fate Merlin fanfiction could be about Merlin guiding a young and inexperienced mage in the modern Fate universe. This could involve him using his ancient magic knowledge to help the new mage face challenges.
Fanfiction.net is also a possibility. There are many Fate Stay Night fanfictions there, and if you specifically search for Merlin - centric ones, you might find some gems. However, the quality can vary more compared to AO3, so you might need to do a bit more sifting through the results.
One interesting aspect is the complex character of Merlin. His mysterious powers and his role as a guide in the story add depth. Another aspect is the unique magic system depicted, which is different from typical magic in other novels. Also, the relationships between the characters, especially those involving Merlin, are full of intrigue.
Fanfiction.net is also a good place. There are many talented writers who post their Fate Merlin fanfictions there. However, the site's search function might be a bit tricky sometimes. So, it's best to be as specific as possible in your search terms.
Perhaps there's a plotline where Merlin discovers that his bond with Arthur is not just a matter of loyalty and friendship, but is actually a magical bond that was created by an ancient magic long before they were born. And as they face various challenges, this bond either strengthens or is put at risk depending on their actions.
One interesting fanfiction could be about Merlin guiding a different Servant through the Holy Grail War in ways not shown in the original. For example, he might use his magic to give a less powerful Servant an edge in battle by revealing hidden strategies of the opponents.
Merlin himself is often a very popular character. His powerful magic and mysterious nature make him a focal point. Writers like to explore his abilities further and put him in different scenarios.