FanficRecs Awesome in a Can
I dismissed this one at first because of a number of spelling and grammar errors in the first few chapters. I was encouraged by others to keep reading past that point however, and I'm glad I did; the author gets a beta around chapter 5 or so and the story improves dramatically after that point. Neoalfa has indicated that he plans to go back and redo those chapters eventually, so until then just muscle through the beginning and get to the good stuff.
This fic does something that very few other stories do, and the ones that do it often do poorly; it focuses on a time period outside of the Grail Wars for a significant part of the story. The first arc focuses on Shirou and Rin teaming up to solve a kidnapping which turns into a much larger problem towards the end of the arc. It's refreshing to see the characters interact in unfamiliar circumstances, and moreso when it becomes apparent how exactly this arc eventually ties in to the Grail War. The climax of the first arc is pulled off beautifully, and was sufficiently epic that I felt the need to open up You Tube and turn on EMIYA while I was reading.
FanficRecs By Caellach Tiger Eye
I haven't looked at this one for a while now, but from what I remember the storyline - concept and execution both - is excellent, particularly after the first few chapters are done and the writing improves (it was always good, it just gets better from there). This is basically what would happen if you turned F/SN into a Reconstruction magic.
FanficRecs Well worth reading
This story starts off with the question "Why didn't Shirou actually do Something to try and fulfill his dream of being a superhero?" and just gets progressively more and more awesome from there. The characters are well written and character development is both omnipresent and reasonable. Things start going off the rails very early on with Shirou running around as the masked vigilante "the Archer" and fighting crime in a beautiful arc that deals with double identities and pulls in Rin Tohsaka in a kidnapping mystery. It spirals completely out of control (in a good way) from there with Shirou becoming one of the earliest participants in the grail war and becomes completely AU when Shirou ends up contracting with a completely different servant from normal in a very believable way. The story does have several characters from Persona used to round out the cast, but knowledge of persona isn't needed to appreciate them.
Countless incidences of Crowning Moment Of Awesome and some beautiful fight scenes round out the litany of reasons to read this fanfic.