Here are a few examples, some from that list, a couple more recently found:
Angels of Light (Forever Knight/Touched by an Angel), by Azar. The "faith" bit is obvious, but it's so deftly handled, with the opposition of the vampire's self-damnation and the fact that grace is still offered to him, if he can only bring himself to see that, and receive it.
Schism (X-Files), also by Azar. Features a Christian OC who isn't obnoxious. Who knew such a thing existed in fanfic?
In a Land of Shadow (The Sentinel/The Professionals), by Gil Hale. I'm not sure this should even be included in this list, but there are coincidences and spiritual hints (The Sentinel, so, visions even) in this fic that stood out strongly to me as direct evidence of God's grace in the world the author has created.
Price to Pay, and particularly its sequel, Truth and Consequences (SG-1, AU from late 5th season), by watervole. This double-header is a great novel anyway, but it also includes the only convincing conversion scene I have ever read in fiction. I am not joking; it flattened me with its truth, and if I wasn't her fangirl before, I am now.
(I was wanting to put rj_anderson's Doctor Who fic "Sacrifice" in here, but it has been removed from the net due to happy profic-writing complications, so. I can live without it. *g*)
My request to you all is to rec in the comments other fics that you think might fit into this catagory. Doesn't have to be faith in the Christian God, per se; I'll take other stuff as well, including fictional religions such as the Prophets of Bajor (Kira's journey of faith has always moved me). But I would be interested to see what kind of list we can scrape up, and what fandoms might be most represented. (I almost included one of vilakins's Blake's 7 fics in this list; and there are others I left out as well, including a few from the Supernatural fandom.)