I guess I will have to contribute some recommendations.
Title:Dear Tohsaka
Author: Tobias
Genre: Drama
Summary: set a few years after the end of UBW, Sakura writes a letter to Rin. There's also a part 2, Dear Emiya and a part 3, Dear Matou.
Pairing(s): none
Link: http://www.fanfiction.net/s/7036433/1/Dear_Tohsaka
Warnings: Bring tissues
Title: Chaos Theory
Author: Moczo
Genre:Adventure/Supernatural
Summary: In one of the many corners of the multiverse, Shirou makes nice with Ilya in their first meeting, thereby changing the entire course of the Holy Grail War.
Pairing(s): Shirou x Ilya.
Link:http://www.fanfiction.net/s/6372400/1/Chaos_Theory
Warnings: be ready to sit down to read for a few hours, you will get hooked.
Title: The Hound and the Blacksmith
Author: Elf
Genre: ... Comedy/80s Buddy Cop?
Summary: One's a Celtic demi-god with a lust for battle and the ladies, the other is a former Counter Guardian who's body is made of swords. Together they fight the forces of evil. Or something.
Pairing(s): Many, Lancer/Ayako is the main one with sides of Archer/Rin and Shirou/Sakura.
Link: http://forums.nrvnqsr.com/showthread...the-Blacksmith
Warnings: None.
Title: Fate/Far Side
Author: Arashi Leonheart
Genre: Drama/Romance
Summary: Kiritsugu takes Shirou to Misaki city on a trip to see a physician for his illness, Years later, with the knowledge of what really happened to his father as well as for nostalgia's sake Shirou takes a trip to Misaki once more.
Pairing(s): Depends on the route you read, you can get Shirou/Hisui, Shirou/Akiha and Shirou/Kohaku
Link: http://forums.nrvnqsr.com/showthread.php/900-Fate-Far-Side
Warnings: There be lemons in this fic.
Also wanna trow my vote for Linatique, That Ever Ilusive Utopia, Shared Resonance of possession Experience and Njeri.
EDIT:
You sniped Chaos Theory out of my hands Kyte, bravo Kyte. Bravo.