I've read a lot of Seishirou/Subaru fic — it's how I got into TB in the first place — and have in the past few years come across some truly great works. This page highlights those fics.
Please heed the warnings on individual works. As with the original canon, not all fics have a happy ending.
nukume dori by leareth
After the Final Day, Subaru finds himself sixteen again and reliving the last few months of the Bet, this time with the knowledge of all that is to come. He knows that Seishirou is the Sakurazukamori, he knows that they are playing a deadly game of love and death - and he knows that Hokuto's life is at stake if he loses.
Read on AO3
Hands down my single favorite fic for this pairing. To quote Mark Oshiro, I love time travel more than most things, and this fic uses the trope to fantastic effect. Watching X!Subaru relive the events of Tokyo Babylon is heartbreaking and beautiful, and the writing is incredible.
Incomplete, but still being written. This fic is updated with lengthy chapters about once or twice a year; I drop everything and read it when it's updated.
Leareth's other works are excellent, as well. I also highly recommend Morning, but her entire archive is worth checking out.
sakura & snow by natalie baan
Subaru decides it is time for him to die. Seishirou disagrees. This is the starting point for a battle that takes place mostly within the mind. Seishirou takes Subaru in, out of a whim, really. He is constantly balancing the fine edge of indifference, curiosity and something he can't quite identify. Although he is good at identifying emotional states, at least when it comes to other people.
Read on author's website
I'm generally a very fast reader — lengthy works, whether published or fanfic, tend to only take me a day or so to read. This fic took me several days to work through simply because I wanted to savor every sentence. The prose is gorgeous.
What makes this fic so remarkable, I think, is that it's written mostly from Seishirou's perspective — and that the writer nails his psyche. Many writers try to do this and fall short, but this Seishirou is one of the most fascinating I've ever read, and it was easy to get caught up in his mind.
Complete. Comes in PG-13 and mature audiences versions, with optional sex scenes.
decagram by akk
The Decagram is basically an attempt to take the canon of Tokyo Babylon and X/1999 as it was given up to X/1999 vol. 18.5 and return it subsequently to the principle of yin and yang rather than the Christian fatalism prevalent in the later books of X.
The focus is firmly on Sakurazuka Seishiro and Sumeragi Subaru, their involvement in bringing these changes to pass, and the resulting relationship between them. However, other canon characters and the history of the clans of Sumeragi and Sakurazuka are explored as well.
Read on AO3
This series is comprised of two completed long fics (36° and Family Matters), as well as a few shorter pieces. A sequel to Family Matters is planned but has not yet begun as of this writing.
What I enjoyed about this series was the focus on, as the summary says, onmyoujitsu and what it means for Seishirou and Subaru. It's a work with a lot of spiritual elements, but they're very interesting and it makes for a fascinating read. 36°, in particular, shows that Subaru and Seishirou aren't all that different after all.
This is a fandom that's almost as old as I am. People don't write much fic for it. If you've got a rec, please send it my way. I like longfic, but I'll read just about anything.