Continua: Neon Genesis Evangelion, Blue Drop (minor appearance)
Status: Essentially complete, epilogue currently dormant
Warnings: Language, sexual content, rape (it's not quite as dark as this warning list makes it seem, though)
Summary: The author doesn't give a summary, so here's mine. An Evangelion self-insert that deconstructs many typical SI tropes in much the same way that Eva did with anime. Follows the plot of the anime up to a point, after which things go completely off the rails and into new territory.
The reason I like it: It's an SI handled far, far better than most. Sure, the guy's a walking firearms encyclopedia, and the gun-focus can get irritating at times, but in general this is an entertaining (if darker and more militaristic) take on Evangelion.
Summary: He hadn't really counted on getting into a pub brawl over the color of his coat on some speck of a planet, or signing up with a crew of petty criminals. Still, he'd always wondered what really happened to those Lost Colonists from Earth...
The reason I like it: I like both series, and have often thought about what would happen if they collided: this is far better than anything I dreamed up! Everyone is almost entirely in-character as far as I can tell, and the plot, if rather generic, is enjoyable and well-thought-out.