Below are some (to name all would alas be a too long list) of my favourite Snape/Hermione fanfics of all time. I highly recommend you check these out (and other fics by the same authors).
An Unwritten Future by Aurette
Still struggling with the aftermath of the war, Hermione decides to leave everything behind to go find herself. She travels further than she could have ever imagined without going anywhere at all. Along the way, she discovers someone she mistakenly thought she'd known...
https://www.fanfiction.net/s/8455295/1/An-Unwritten-Future
This is my favourite time-travel fic of all times. Come for the seriously adorable young Snape, stay for the wit and the romance (and perhaps the most clever reason for time-travelling I’ve read).
Before the Dawn by Snarkyroxy
In her seventh year, a late night discovery changes Hermione Granger's views on a great many things. Severus Snape is just one of them.
http://ashwinder.sycophanthex.com/viewstory.php?sid=10633&i=1
This story is responsible for getting me hooked on Snape/Hermione as a pairing. Since I first read it 10 years ago, I’ve read and re-read it at least half a dozen times. Written before the release of HBP, it’s a refreshing read if one’s just come of a bender reading DH-divergent fics. The romance is the best kind of standing-too-close and stealing-glances without it feeling out of character. 10 out of 10 would recommend.
Camerado by MillieJoan
Hermione seeks knowledge from a reluctant Snape in order to help the War effort. What she receives is more than either of them expected.
https://www.fanfiction.net/s/5089614/1/Camerado
Speaking of DH-divergent fics; this is one of my absolute favourites in that category. The characterisation is sublime; there are layers upon layers to these characters that are equally fascinating and heartbreaking. This story feels real, for lack of a better word, there is no separation from fic and reader, no shying away from the harsher side of things. The characters are lovable for all their flaws, and you feel everything that happens just as deeply as they do.
Do Not Go Gentle by SenLinYu
It was subtle at first. For the first several months, she assumed it was merely the stress of the war; for the next several months, she assumed it was the stress of the trials; then when winter approached, she assumed it was stress from school.She kept assuming it was stress until she was walking to the cabinet to retrieve her supplies for Potions class and the walls began closing in, wobbling and swallowing her up.When she woke again, she was in the Hogwarts hospital ward.Severus Snape stood at her bedside, staring down at her with an expression of profound irritation.
https://archiveofourown.org/works/22065178?view_full_work=true
This fic is a WIP, written wonderfully by SenLinYu (who usually writes Dramione fics). I don’t want to give anything away for those of you who haven’t read this yet, but it’s heartbreakingly beautiful. Seldom do fics make me cry, but this has made me done so on several occasions.