Stutter and Stumble by sparkley-tangerine (http://www.fanfiction.net/s/5185218/1/bStutter_b_and_bStumble_b)
Summery: On October 31st, 1981 Harry Potter's parents died in one tragic and unforgettable night at the hand of Voldemort. No one questioned it, there was no other possible suspects for such a crime. Twenty-three years later, Harry's beginning to find that maybe jumping to conclusions wasn't the brightest idea and he gets the feeling that maybe this John Winchester would agree.*dean/harry HP Xover*

An Unexpected Debt by dharkcharlotte (http://www.tthfanfic.org/Story-12839/dharkcharlotte+An+Unexpected+Debt.htm)
Summery: An unusual alliance leads to an unexpected debt. *Dean/Hermione HP Xover*

Second Chance by Lizzy Pheonix (http://www.fanfiction.net/s/8545076/1/Second-Chance)
Summery:Ten Years ago Dean spent three days in bliss but when he learned the truth about his lover he couldn't deal. Ten years later a hunt brings them together again will Dean make the same choice *dean/harry HP Xover*

Asmodeus by She Who Cannot Be Turned (http://www.fanfiction.net/s/5570636/1/Asmodeus)
Summery: Harry, the last of his kind, escapes from Britain after a long and gruelling battle and heads for America. He is completely unaware of the danger he has just thrown himself into. *dean/harry HP Xover*

Hunters and Heroes by TamrynEradani (http://archiveofourown.org/series/26114)
Summery: Clint and Dean meet when Clint's a beginning agent, and Dean's hunting on his own, because his dad's off doing something and Sam's in college. They keep in touch as Clint takes out his family and Dean dies for his, and they form a friendship that becomes something more.
With the apocalypse averted and an alien invasion twarted, things should get easier, but with an invitation for the Winchesters to live at Stark Tower, Sam falling in love with an assassin, and Castiel using Steve Rogers as a study in humans, Dean thinks his life has actually gotten more complicated. *dean/clint avengers Xover*

The Time Has Come to be Gone by jujuberry136 (http://jujuberry136.livejournal.com/48428.html)
Summery: When Aaron Hotchner stepped into the interrogation room to interview one of the FBI’s most wanted unexpectedly apprehended earlier in the afternoon, he never thought the evening would end with bloodshed and rock references. *Gen CM Xover*

Nightmares in Dakota by scarletsptember (http://archiveofourown.org/works/428355/chapters/721888)
Summery: South Dakota wasn't anything special but it was the perfect place for Harry and Teddy to start over at. Nothing was going to get them here. *dean/harry HP Xover*


Other Recommended Xovers:

Wolverines, Wendigos and Winchesters By SciFiNutTX (https://www.fanfiction.net/s/5155714/1/Wolverines-Wendigos-and-Winchesters)
Summery: Dean meets Wolverine during a solo hunt, which leads to friendship and a new job. *DEAM/OFC, X-Men xover*

Migratory Birds by nekare (http://archiveofourown.org/works/181861)
Summary: When the end comes, one brother is on one side, and the other on the opposite. *Gen X-men Xover*

Panta Rhei by Notasmuch (http://archiveofourown.org/works/185927/chapters/273607)
Summery:This is a story of how Jensen and Dean met, hooked up, started falling in love, and what happened during and after, way back in 2001. *Dean/Jensen*