Elyandarin

Cool, found some good stories in this thread. 

Since it seems to be more or less "anything goes", here's a few I enjoy and didn't see in the summary: 

Original fiction: 

Billy-Bob, SPACE TRUCKER

Silly but highly entertaining HFY sci-fi story. A slovenly Space Trucker gets involved in galactic politics and solves it the way American culture taught him these things should be solved: with acts of extreme violence set to a rocking soundtrack... 

Interviewing Leather 

Intrepid reporter interviews up-and-coming supervillain. This apparently includes getting kidnapped. 

Three Worlds Collide 

Brainy ethical dilemmas in space: as first contact is made, we find that our new alien friends are... differently moral. [Mature content]

Of Heroes and Villains

Batmanesque superhero's life takes a turn for the weirder after a plant-based villainess catches him cross-dressing.  [Mature content]

Fanfiction:

Harry Potter and the Methods of Rationality

Smarter characters, more SCIENCE. A Harry Potter raised as a scientist goes to Hogwarts, and becomes best friends with Hermione, Draco and Professor Quirrel. 

Time Braid

Naruto Groundhog-Day scenario with Sakura as the remarkably non-annoying main character. [Content: violence, brainwashing etc. Mature]

Big Human On Campus

Ranma½ / Rosario+Vampire cross-over. In Youkai Academy, overpowered rage-prone monsters are packed together in a school with the intent of teaching them to get along in modern society and/or killing them in the process. (As if the threat from fellow students wasn't enough, staff members include the likes of Jadeite, Franken Fran and Richard). It turns out Ranma fits in surprisingly well. [Comedic sociopathy]

MLP Loops

MLP Groundhog-Day loop with many, many crossovers.