This will be a long list...
First off, a recommendation:
Into the Rain by RadiantBeam
At its core, a "what if" fic that centers on Rin finding Sakura in HF before Shirou can, resulting in a more immediate acceptance of her sisterly feelings. Followed by awakening of feelings that aren't really appropriate for sisters, although Tokiomi would probably be proud of how well she's decided to treat Sakura as if she really were from another family entirely... Contains RadiantBeam's usual trademark skill at evoking romantic feelings combined with plenty of well-drawn imagery; the scene of Rin at her father's grave is exceptionally well-done. Also Shirou may be getting the best consolation prize ever for losing his love interest.
(Seriously, RB, you need to finish this one!)
While on the topic of RadiantBeam, I note that "Moonlight on Steel" is listed among the one-shots; it's actually four chapters. (As is Objective: Emiya and its six parts)
Moving on to Moczo:
Mind of Aluminum
Rin teams up with Shinji and finds that, amazingly enough, he really has something to offer that will guide her to victory in the Holy Grail War! Because even if it wasn't as funny as hell, any fic that contains the line "… are you suggesting we shoot Shinji out of a catapult to spread disease? Because I can get behind that." should get a rec for that alone.
And also by Sir Moc of Zo, The Importance of Proper Communication A funny one-shot about the confrontations in Eps. 14-15 of Fate/Zero, Tokiomi/Kariya and Berserker/Gil. Because Happiness Worms are, surprisingly, not a thing!
Also, +1 to Lunatique (Best. Oneshot. Ever.), Chaos Theory, The Hill of Swords (Don't kill me!), Remember, Fate/Far Side, Shinderella, Steel and Cherry Blossoms, Of Leaves and Lilacs, What If (Almost) Everybody Was Shirou's Servant, Daughter of Shinigami, Sick Time, Objective: Emiya, and Moonlight on Steel.
-1 to Nerve Damage. The mere phrase "Shirou summons four Sabers" makes me want to reach for the barf bag even before we get to the actual fic.