These are gen recs especially starring Hermione Granger. If any fics about her parents turn up, they'll be included here also. Consider them pure gen unless otherwise noted.
A Run in Tights (PG-13) by cawti. Pure gen, except for leering. The Trio has to get to Platform 9 and 3/4 in time to catch the Hogwarts Express, but Death Eaters are everywhere. So how do they elude them? By dressing as Muggle schoolgirls, of course. This fic is cute and fun, but still manages to show the danger they're in. Long one shot.
An Unlikely Proposal (PG) by Expelliarmus. Hermione goes a bit too far back with her Time Turner and runs into Barty Crouch Sr. Cool premise with great execution. One shot.
Bright Girls Blush (G) by DebbieB. Minerva and Hermione have a talk about Hermione's plans in life. Quite fluffy. One shot.
Chance Encounters (G?) by Arabella. The Dursleys go to London and drag Harry along, where he runs into a few people who will be important to him later in life. Cute. One shot.
Corpus Incendio (R) by julia_fractal. Hermione begins to delve into the history of Magical-Muggle interaction. Dark. Short one shot.
Fine With Her (PG) by Laura Smith. Hermione's early life, and how she feels when she gets her Letter. I'm not sure if Hermione is really this smart, but other than that I like her characterization. One shot.
The First Signs of Magic Series (PG?) by Icarus. So far there's Draco, Hermione, and Snape. It's pretty self-explanatory: the first time these three displayed powers. Fluff, humor, and angst. Each is a one shot.
Five Dead Women (R) by Snegurochka. Some very, very minor het. This fic explores the link between several Potterverse women and what they had in commmon. Dark. One shot.
Flitterblooms and Firewhiskey (G) by Red Monster and michelle_31a. We all know Hermione doesn't care for Luna. So how did she manage to ask Luna to set up the Quibbler interview? Chaptered.
Harry Potter and the Muggle Toy Store (PG) by MadisonS. Includes a reference to H/Hr. Harry, Hermione, and Ron go to a toy store and see themselves. I like Elsie. One shot.
Hermione's Scrapbook (PG) by Eliane Fraser. At Grimmauld Place, Hermione pulls out her scrapbook and reflects on the pictures therein. One shot.
I've Read Magick Most Evile (M) by Janice Chess. Death Eaters and ritualistic cannibalism. Rather dark, obviously. One shot.
The Language that God Speaks (PG-13) by Liz Barr. Hints of R/Hr and what might be Snape/Lily if you squint. It's a crossover with Sandman, but you should be able to follow it even if you haven't read those novels. Hermione finds notes for an experimental potion allowing one to access the Dreaming. Hermione, Snape. One shot. There's also a one shot remix here that has a teeny bit more Snape/Lily.
The Last Mudblood (PG-13/R) by furiosity. Voldemort has won the war. Neville Longbottom is a Death Eater looking for Hermione Granger. But things are not always as they seem. One shot.
Luna's Friendship (G) by michelle_31a. Hermione and Luna have a talk in the Hospital Wing at the end of OotP. It does a good job of resolving their issues. One shot.
Midnight Confessions (PG) by Diricawl. It could be pre-R/Hr, or it could just be two friends talking and bickering. Ron and Hermione talking in the Hospital Wing after the MoM battle. One shot.
Names (PG-13) by Penguin. As Harry languishes in St. Mungo's, Hermione tries to identify what she is feeling. Angsty. One shot.
Nice Work If You Can Get It (PG) by Kay Taylor. Hermione gets an office job for her Muggle Studies class. The end turns it into a completely different fic. One shot.
Not Just for Christmas (G) by Leni Jess. Okay, this *not* a gen fic if you consider cats hooking up to be romance, but it *is* gen fic if you only count humans. Anyway, Crookshanks decides that he wants a mate. Cute and fluffy. One shot.
One Lump or Two, Mr. FloppyEars? (G) by Write_away_the_pain. Six-year-old Hermione prepares for some very important guests. Incredibly sweet. One shot.
The Only Thing We Have To Fear (PG-13?) by VoxMaille. Perhaps Hermione's Boggart wasn't actually bad grades after all. Sniffly. One shot.
Oubliette (PG?) by The Pearl. Futurefic, and absolutely heart-wrenching once you realize what's going on. One shot.
Ravenclaw (G) by fourth_rose. A member of Ravenclaw thinks about her house. Short one shot.
Sanity (R) by sionann. Hermione is tortured. Quite dark. Short one shot.
Something Missing (PG) by Eustasia Vye. Hermione tries to remember, but it hurts so much. One shot.
To Fly (PG-13) by Amber. As Harry and Ron are out fighting Voldemort, Hermione researches in the library and fights her own battles. Angsty. One shot.
Things That Don't Exist (PG-13) by shadoed. A Muggle notices a striking girl in the library. Short one shot.
Unsticking the Shadow (PG-13?) by Pogrebin. Voldemort gives an interview, and no one can understand why Hermione is so worried about what he says. This fic shows how easily people and their prejudices can be manipulated. It's scary. One shot.
Walking Shadow (PG-13) by Pogrebin. Harry has a past relationship with Gabrielle Delacour. Surreal and meta, as so many of Pogrebin's fics are. It's a story told backwards, of the second choice that Harry made, aided by Hermione. Weird, in a good way. Long one shot.