Definitely 'Batman: Year One'. Although Scarecrow doesn't have a huge role, his cameo and the implications of his existence in Gotham at that time are interesting. It sets the stage for future encounters. Also, 'Scarecrow: Year One' which focuses specifically on his origin story. It shows how he became the master of fear that he is in the Batman universe.
One of the best Scarecrow stories is 'The Long Halloween'. In it, Scarecrow adds to the overall sense of dread and mystery in Gotham. His fear toxin is used to great effect, making it a great read for Batman fans.
Fear is the most common theme. Since Scarecrow is all about inducing fear, it's often central in these fanfictions. Writers explore how Batman overcomes or is affected by the extreme fear that Scarecrow creates.
One of the best is 'Batman: The Long Halloween'. It features Scarecrow among other iconic Batman villains. The story is a noir - style mystery that unfolds over the course of a year, with holidays as a backdrop. It delves deep into the criminal underworld of Gotham and shows how Scarecrow fits into that dark tapestry.
In some fanfictions, Scarecrow is often depicted as a formidable foe to Batman. His fear toxins play a major role. Batman has to constantly overcome the extreme fears that Scarecrow induces. For example, in certain stories, Scarecrow may target Batman's deepest traumas, like the death of his parents, and use that to try and break him. This creates a very intense dynamic where Batman has to rely on his willpower and detective skills to outwit Scarecrow.
Batman would probably first try to contain the situation. He'd use his resources as Bruce Wayne to spread misinformation or counter the revelation. He might also go on the offensive against Scarecrow to stop him from spreading the news further.
The plot mainly revolves around Batman's encounters with Scarecrow. Scarecrow uses his fear toxins to spread chaos in Arkham. Batman has to face his own fears while trying to stop Scarecrow from causing more harm to the city.
'Batman: No Man's Land' is also a great pick. The story takes place in a Gotham that has been cut off from the rest of the world. Scarecrow thrives in this lawless and desolate environment. It gives a different perspective on his character as he takes advantage of the fear and despair around him.
One popular theme is the exploration of fear. Since Scarecrow is the master of fear, fanfictions often delve deep into how different characters, especially Batman, experience and overcome fear. Another theme is the battle of wits. Batman is a brilliant detective and Scarecrow is a cunning adversary, so their mental duels are a big draw.