Most of these are crossovers:
Bats and Wizards - a pair of neat short stories crossing the Batman and Young Wizards (YA fiction) universes.
A Widow's Tale - series of Avengers/Stargate Atlantis crossover stories in which Natasha Romanoff is secretly John Sheppard's mother. WIP, about 340k words over several stories.
The Shield Agent's Wife - series of Avengers stories about Agent Phil Coulson's relationship with the cellist briefly mentioned in The Avengers. Not very canon compliant for Agents of SHIELD, especially their story about this character, but a lot of fun.
Eighth Dimension And Beyond - There isn't much Buckaroo Banzai fanfic. This series is about the best of it, crossovers with Eureka, Back to the Future, and Firefly.
Stars, Rain, Sun, Moon - another Young Wizards crossover series (one long story and two shorts), this time with The Avengers.
Elementary, My Dear Sherlock (WIP) - Sherlock/Elementary crossover in which John Watson and Jane Watson somehow find themselves in the wrong universes.
By Any Other Name - Avengers/Hansel & Gretel: Witch Hunters crossover - Hansel and Clint Barton (both played by Jeremy Renner) are magically mind-swapped. Adult themes!
