My favorite fan fiction of all time is 'Take My Heart Away' by Hatsu. It's Hermione/Tom Riddle, and it's incredible in character and refreshing. It's the only Dark/Angst fiction I've liked, and it made me cry. Go read it!
A Moment, A Love by jenny b
Rated: Professors [Reviews - 179]
Summary: 
A Sleepwalk to Remember by Lady Knightly
Rated: 6th-7th Years [Reviews - 943]
Summary: For once in her life, Hermione is faced with a problem she does not know how to solve...
Our Little Secret by Kerichi
Rated: 6th-7th Years [Reviews - 416]
Summary:
It was like a wizard tale. The clever Slytherin helps a hag who later repays the debt. Except that Rose Weasley wasn't a hag, and Scorpius didn't expect to call in the favour.
*Winner of the 2010 Next Generation QSQ award*
Nessun Dorma by Soap
Rated: 6th-7th Years [Reviews - 176]
Summary: Rebuilding after the final battle of Hogwarts was difficult for everyone, but even moreso for one person in particular. How will Remus recover after so much sadness in his life?
Post Deathly Hallows - Spoilers! Slightly AU. Remus/Hermione.
Clair De Lune by Astrid Skywalker
Rated: 6th-7th Years [Reviews - 386]
Summary:
It was full moon when the Dark Lord sealed a part of his soul within a magical amulet, and then broke it in half. One half was left to the faithful werewolves to guard. The other half was tossed into the impenetrable depths of time where no one but him could get it. When the first half has been found, the Order of the Phoenix selects Hermione Granger to go back into the past to search for the missing piece. What is waiting for her is a brutal task that will test her beyond her limits, and an undying love that extends beyond the boundaries of time.
RL/HG, Post-HBP
No werewolves were harmed in the making of this story.
Update (9 May): Chapter 17, Burning, is up! Enjoy!
Take My Heart Away by Hatusu
Rated: 6th-7th Years [Reviews - 958]
Summary: Hermione goes back in time with one mission: to kill Tom Riddle before he ever comes to power. A difficult task, correct? An impossible one, she realizes, as a love between them grows stronger than anything she has ever known. Now Hermione has a choice to make. Will she condemn the Wizarding world to almost certain destruction, or will she take the life of the one boy she has ever loved?
Padfoot Prohibited by Liveley
Rated: [Reviews - 825]
Summary: Giving high school essays a Marauder twist, this fiction is centered around the idea that some seniors in high school are require to write a letter to incoming freshman before they graduate. At Hogwarts, Seventh Years are given an assignment to write such a letter for the new First Years. Sirius decides to actually take an assignment, well seriously...sort of. He decides to look back on his entire Hogwarts years and write down his list of things not to do at Hogwarts.
Master of Enchantment by Subversa
Rated: Professors [Reviews - 196]
Summary: Winner in the Best Mid-Length Story and Best Romance categories in Round One of the Most Potente Passions SSHG Awards.
It begins the summer after Seventh Year, when the war is raging on, with an unexpected moment of tenderness. What is this inexplicable feeling Hermione experiences? And how can she get Snape to discuss it with her, when all he wants to do is avoid her? Rating for last chapter, only.
