Big things are happening on TV Tropes! New admins, new designs, fewer ads, mobile versions, beta testing opportunities, thematic discovery engine, fun trope tools and toys, and much more - Learn how to help here and discuss here.
Enter the Dragon, which is a Harry Potter fanfic which will eventually cross over with Shadowrun, in which Harry is turned into, well, a dragon by a freak accident at the age of eight. Incomplete; currently finished with the parts before his attendance at Hogwarts, which basically consist of him living on the Hogwarts grounds (because who else is equipped to deal with a pre-teen Greater Dragon who eats meat, every plant that grows, random potions ingredients, and sheet steel, and drinks, depending on mood, water or gasoline?) and having interesting conversations with those who are aware of his presence there.
The Book of Dobby, which is an AU diverging at the end of Harry's fourth year, and also apparently a crossover with Girl Genius. Harry intends to take the fight to Voldemort in a way he is not equipped to understand. Dobby is organizing the house-elves into as close a replica as possible of the RAF circa 1940, and the Gringotts goblins are apparently the Jaegers. It's crack, but highly entertaining; incomplete.
Top Dog, a really huge Mega Crossover universe patterned in form after Undocumented Features. The main continuities are Enter the Fnords, which is Harry Potter with a severely traumatized and Bad AssAnti-Hero Harry in a magical world upgraded to fit into Top Dog's intergalactic politics; Biker Half, which is Ranma ½ with Ranma the heir unaware of one of the strongest Amerai clans; and A Fox in Tokyo, which is Naruto, with guns and Claymore mines, in a Konohagakure transplanted into the Nerima of Biker Half. Epic storyline, and a wonderful series of funny moments as you see the canon universes fitting into the crossover.