One popular plot idea is that the characters from Supernatural, like Sam and Dean, end up in the Flash's Central City while chasing a supernatural entity that has some connection to the particle accelerator explosion. Another could be that Barry Allen, as the Flash, somehow gets transported to the Supernatural universe and has to deal with demons and angels. A third idea might be a joint mission where the two teams have to stop a powerful villain who is using both magic from the Supernatural world and advanced science from the Flash's world.
One idea could be that the Winchesters are hunting a meta - human in Central City who has powers similar to a demon. The Flash team tries to stop them from killing the meta - human, thinking they are just bad guys. Another could be a time - travel situation where Barry accidentally travels to a world where the Supernatural events are real and has to team up with Sam and Dean to get back home. A third idea is that a powerful witch from the Supernatural universe uses her magic to create chaos in Central City, and the Flash and his friends need the help of the Winchesters to defeat her.
Well, a lot of times the plot ideas revolve around the characters' different approaches to the unknown. Mulder's eager belief in the paranormal in 'X - Files' and the Winchesters' more hands - on, hunter - like approach in 'Supernatural' can create interesting dynamics. A common plot might be that a strange entity is causing disappearances, and it has characteristics of both an alien and a demon. The two sets of characters would then have to figure out how to work together to stop it, with Scully providing the scientific perspective and the Winchesters their knowledge of the occult.
Some fanfictions might pair Castiel and Cisco Ramon. Castiel's otherworldly nature and Cisco's scientific mind could lead to some really interesting interactions. For example, Cisco could be fascinated by Castiel's angelic powers and try to find a scientific explanation for them, while Castiel could be intrigued by Cisco's tech - savvy ways.
One idea could be that a supernatural entity from the Supernatural world somehow ends up in Central City and starts causing chaos that only the Flash's speed can help contain. For example, a demon that can possess multiple people at once and the Flash has to use his speed to track down all the possessed bodies before the demon can complete a dark ritual.
One interesting plot idea could be a battle between the hunters from Supernatural and the vampires from Vampire Diaries. Maybe the Winchesters end up in Mystic Falls and think all the vampires there need to be hunted. Another idea is a character swap. For example, Castiel could end up in the Vampire Diaries world and interact with the characters there in a very different way compared to his usual interactions in Supernatural. A third idea could be a joint mission to fight a greater evil that threatens both universes, like an ancient demon that wants to use the power of the vampires in Vampire Diaries and the magic from Supernatural for its own dark purposes.
One idea could be a crossover with another superhero show where The Flash has to team up with their heroes to stop a multiverse - threatening villain. Maybe he teams up with Arrow and they have to combine their skills to take on a speedster from another dimension who can also turn invisible.
One popular storyline is when Flash and Supergirl team up to fight a common enemy from another dimension. This allows for a lot of action and showcases their different powers working together.
One idea could be that the Winchester brothers from Supernatural are investigating a series of strange murders in Gotham City. They cross paths with Batman who initially is suspicious of them. Eventually, they realize that a demon is behind the killings and they team up. Batman provides his detective skills and combat abilities while the Winchesters use their knowledge of the supernatural to defeat the demon.
A plot could involve the Avengers trying to understand the Flash's powers. Tony Stark might be especially intrigued and try to create technology to mimic the speed force. Meanwhile, the Flash could be in awe of the Avengers' different abilities and learn new ways to use his speed from them. For example, he could learn combat strategies from Captain America or how to better control his powers from Doctor Strange. And then they all have to face a threat that only their combined powers can defeat, like a cosmic entity that is draining the life force of both their universes.
One idea could be that the Flash has to help Batman track down a super - villain who has the ability to manipulate time. Since the Flash is a speedster, he can move through time - altered situations more easily. Another plot could involve Batman creating a new gadget to counter a meta - human threat, and the Flash accidentally gets caught in its test run, causing some wacky time - space anomalies that they have to work together to fix.