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 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.
One plot idea could be that a character from Flash, like Barry Allen, somehow gets zapped into the Glee universe. He could be confused by all the singing and dancing at first, but then use his speed to help the Glee club prepare for a big competition in a very short time. For example, he could quickly gather all the necessary props or help the members with their choreography by demonstrating moves at super - speed.
One idea could be that Flash and Supergirl team up to stop a powerful alien villain who is causing chaos across both their cities. The villain could have the ability to manipulate time and space, which would make it a real challenge for the two heroes.
One idea could be that the Avengers have to deal with a supernatural force that is causing chaos in the city. Maybe it's a powerful demon that they can't defeat with their usual weapons and tactics. They then seek help from the Supernatural world, like Sam and Dean Winchester, who teach them about exorcisms and using holy water.
A cross - over could involve a curse in the 'Arrow' world that has a supernatural origin. Oliver Queen and his team seek the help of Sam and Dean Winchester who are experts in dealing with the supernatural. Along the way, there are clashes in their methods of operation but they gradually learn to trust each other and combine their skills to break the curse.
One idea could be a crossover with 'Doctor Who'. The Doctor and the Winchesters could team up to fight a time - traveling demon. Another could be a crossover with 'Buffy the Vampire Slayer', where Buffy and the boys from Supernatural join forces against a powerful vampire coven that has some sort of connection to the supernatural underworld in both universes. And a crossover with 'The X - Files' would also be cool, with Mulder and Scully investigating a case that turns out to be related to the monsters the Winchesters usually hunt.
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 idea could be to have the characters from Glee perform at a Central City event in the Flash universe. They could sing a song to boost the morale of the citizens during a time of crisis.
A really cool plot might be that the forces of Hell in Supernatural are trying to take over Gravity Falls because of its unique supernatural properties. Sam and Dean, along with Dipper and Mabel, would need to use their combined knowledge and skills. Sam's research abilities and Dean's combat skills, along with Dipper's knowledge of the town's secrets and Mabel's out - of - the - box thinking, to stop the demonic invasion.
One idea could be that Danny and the Winchester brothers team up to fight a ghost that is causing chaos in both the Ghost Zone and the human world. Maybe it's a powerful entity that has the ability to cross between dimensions easily.