The best I have read so far was link, 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 :)
The other good fic is link, but this one is quite heavy with smut and BDSM, so if you don't like the theme, I suggest not reading.
There was also another one, called Invitation to Detention, but it's been pulled of from Ashwinder and now I can't find it anywhere :(
Besides that there's a lot of great fics on Ashwinder and FF.net, but way too many to list them al. I just listed those that made the biggest impression on me.
this is the third one I am re-reading this one and I love it so I thought I'll mention it:
link. Great story (even though I always skip the Snape/Lily thing)
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 link
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 think the best SS/HG fanfic in English is link, 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, link (Sielujen puutarha) and link (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: link. 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!
My favorite is called 'The Closet'. It's where Snape and Hermione are trapped in a small closet. It's a oneshot.
I like Hello Muddah, Helloh Faddah.
I also like Truth or Dare
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.