The best I have read so far was Out Of Depths, it's pretty long, but it's probably the only fanfic that manages to keep Severus Snape in character from the beginning till the end and at the same time make him quite a romantic man. Hermione might be a bit OOC, but I kinda like her that way :)
I think the best SS/HG fanfic in English is Solitaire, but I have also read a few of really good Finnish fanfics.
We have a fantastic fanfiction writer, pseudonymous Aura Illumina, and she have written a couple of gorgeous SS/HG fanfics, The Garden of Minds (Sielujen puutarha) and Gentle Rain (Lempeä sade). You can find them from her blog, for example, also in English. These links take you there.
I have also read an awesome Finnish fic called "Putoaminen" from a Finnish Harry Potter ficforum, Finfanfun, but it isn't available in English and I'm not sure does I have rights to link it without it's writers permission. But if you want to read it in Finnish, you can register to finfanfun.fi and read it there.
//I'm terribly sorry if there is some spelling mistakes.
Pretty much anything written by Ms_figg. I have an obsession with her stories and have read them many times each. Her best ones though would be Daddy Dearest and Becoming familiar with a man of misery.
I've read many, many Snape/Hermione fanfics, but the one that stands as my all-time favorite is "A Walking Shadow" by Ariadne AWS, found here: www.fanfiction.net/s/2848602/1/bA_b_bWalking_b_bShadow_b. It's not very explicit, but there are some romantic scenes which just make me whimper--for example, there's a scene where he touches her not with his hands, but only with a black silk cloak...*whew*! Also, the exchanges between the paintings of Phineas Nigellus and Mrs. Black are hilarious!
The very first fic I read of ss and hg has been my favorite story for years. If you are looking for something to read, I highly recommend this. (student/teacher) if you ever read it let me know, I would love to know if I just love it because it was my first or if it really was good. Haha
There's never just one favorite fanfic, at least for me. Every author has a unique way to tell stories or it's at least the idea behind the fic that captures me. I prefer explicit erotic content in combination romance/drama. My favorite stories are Caged Bird Sings, Second Life, The Love You Take, Yea Though I Walk, Care of Magical Creatures and lots more.
I like Out of the Depths, Pride of Time and The Five Winters. It's impossible to pick just one favorite, I also love Heart Over Mind, Chasing the Sun, Cloak of Courage..and the list goes on. BTW, these can all be found at ff.net.