On the Threshold We All Stood, for Neon Genesis Evangelion. Some would say that's it's little more than original spy fiction with some names from NGE sprinkled around. Some would have to take a closer look.
Mass Effect: Conception. The most bleak, depressing, and hopeless work I've ever read.
Eternal (MLP:FIM) The epilogue makes me cry.
Aeon Entelechy Evangelion, the story of Neon Genesis Evangelion set in a homebrewed variant of the CthulhuTech setting. I especially love the equivalent of the Gaghiel fight. It was one of the weaker Angels in canon, but here, it is absolutely horrifying. Unfortunately incomplete and on effective hiatus.
A Green Sun Illuminates The Void, a crossover between Familiar of Zero and Exalted, by the same author as the abovementioned AEE. I didn't know or like FoZ much before, but this story keeps me hooked. Incomplete but ongoing.
