I'm a huge fan of HPMOR (Harry Potter and the Methods of Rationality), which I think is far superior to the original.
There's also "Following the Phoenix," which is an offshoot of the HPMOR story, I enjoyed that, too.
A friend recently mentioned "The Boy Who Yid," which is fascinating, although incomplete and no updates within the last year or so.
Then there's the "Herschel Pinter," which is comic relief (depending on your sense of humor), a uber-yeshivish written version.
Any other good ones out there that I've missed?