I love myself a good fanfic, as long as it's entertaining. If I find a good fanfic I'll put it here.
Thinking in Little Green Boxes
Description: Harry Potter is raised by Deadpool. Hilarity ensues (for example, Deadpool steals Doctor Doom's Visa and goes on a shopping spree).
Description: A massive crossover between various Nintendo and Capcom characters, as they fight over the future of child with mysterious powers. (Found this on the FanRecs page of Super Smash Bros. on TVTropes.org)
Description: Crossover with the SCP Foundation.
Paper Mario: The Temple of the Sun
Description: Paper Mario story that takes place after Super Paper Mario. Unlike in the games Mario is both talkative and snarky.
Chronicles of the Stars (Part 1) (Part 2) (Part 3)
Description: Three-part series that has the Mario bros team up with the Wario bros.
Description: Turbo from Wreck-It Ralph is sent back in time to TurboTime in the year 1987 after his demise in Sugar Rush. Will he make the same choices?
Doctor Doom travels through Kanto with a Magikarp as his starter
Description: Exactly as the title says, it's Doctor Doom of Marvel Universe meets Pokemon. Considering that it's Doctor Doom, it's quite violent.
Pokemon Mystery Dungeon 2: A Novelization
Description: The novelization of the Explorers games, adding new backstory in the process.
Has a sequel called Pokemon Mystery Dungeon: Life in Flames