They can't all be Mary Sues, can they? This list is for fanfictions starring original characters, or OCs. Consider them pure gen unless otherwise noted.
1975 (PG-13) by Narcissa Malfoy. This has relationships in it, but they're commiserate with everyone being 15 and aren't really the focus of the fic. It's in the middle of being revised to be OotP-compliant, so after the fifth chapter some names change and a subplot is dropped. Novel length. The sequel, Dust and Shadow, has one chapter up now.
A Gutter Rat's Tale (R) by Minnionette. Canon James/Lily, but otherwise pure gen. The tale of how a gutter rat was adopted into the Potter family and christened Severus Snape, and his further adventures. Not OotP-compliant, of course, but quite well plotted and thought out. Novel length.
A Paris Tradition (PG-13) by Framling. When the ads in the Daily Prophet don't turn up anyone worth bothering about, Dumbledore and McGonagall make their own decision about who they want teaching DaDA. The problem is, he's nowhere to be found. Has a cast of wolves, owls, elephants with attitude, and one unhappy mouse. WIP, likely to be novel length.
A Matter of Perception (PG) by Rosie Red. A Muggle stumbles into a certain pub. One shot.
And Miles To Go Before I Sleep (PG) by Paracelsus. Minor H/G reference. A physician in New Zealand dreams of a battle between good and evil, and wakes up to find an amnesiac patient under her care. Chaptered.
The Apparating Instructor (PG-13) by tybalt-quin. Neville goes in for an apparating lesson. Funny and cute. One shot.
The Arithmancer's Apprentice (PG) by Alec Dossestor and Teri Krenek. When Tom Riddle is instructed by his Arithmancy professor to retrieve a certain ring from Mountwarlock Park, he falls into a tangle of danger and political intrigue. I love the world that the authors sketch out here. The sequel is Imperius Quidditch (PG), in which Tom is taken by his mentor to play a ruthless game. Both fics are novel length.
Black Gold (R) by Pobregin. This one's sort of on the edge; it has relationships, but I think it's gen enough, and it's definitely not a shipping fic. ‘There is only oil, more precious than gold & certain types of information.’ It is 1942. While German tanks trundle over White Russia, Gerald Wilkes, traitor to England and adulterer, is about to be betrayed by his wife. A twisted historical chronicle of how Grindelwald lost the War, complete with Marxist Muggle-huggers, shifting tenses, corrupt Archbishops, 3 Acts and a guest appearance by Adolf Hitler. Long one shot.
Bringing Up Tommy Riddle (G) by Auror_Lib. Voldemort meets with someone even more powerful that he is. Silly. One shot.
The Bureau of Loopholes (T) by Gileonan. Pure gen. MWPP, as well as many others, get caught up in the struggle for the rights of humans with accidentally- inflicted preternatural conditions. Has some interesting ideas about the early days of the Death Eaters, as well. Novel length, abandoned WIP.
Can't Be Held Responsible (PG-13) by Amy Fortuna. One or two crushes are mentioned. Minerva MacDonald reflects on one of the patients under her care. Wonderfully meta. One shot.
The Chocolate Frog War (G) by Leni Jess. Stuck in Azkaban, Snape is drawn into an escalating conflict with his jailors. Clever. One shot.
Christmas on the Dail Llewellyn Ward (PG) by Emily Anne. I have no idea why I didn't rec this before; it's definitely an HP classic. During OotP, Remus talks to the werewolf in the bed next to Arthur Weasley's. Great characterization and dialogue. One shot.
Dazzle (G) by Gehayi. Little Regulus is afraid of the lightning, but this time someone is there to comfort him. Angsty. One shot.
Don't Badger the Badger (PG) by Viridis. Sorting Hat sang: "Good Hufflepuff, she took the rest, and taught them all she knew." Hufflepuffs are quiet, inoffensive and generally uninteresting, aren't they? But they have a badger in their coat of arms. And one should really never, never badger the badger. Reminiscent of Poe. One shot.
The Durmstrang Chronicles (R-ish) by Loup Noir. Okay, this is a bit complicated. The first two are mostly gen; there's bits of (uncondoned by the protagonist) teacher/older student relationships. The later Chronicles tend to be either borderline or not gen at all, but they're all very good. This is the story of the Dark Arts professors at Durmstrang. It's about as dark as the name implies. Full of interesting and well rounded OCs. Novel length fics and one shots.
Eshu's Daughter (PG?) by Tapestry. Kit Ellsington, an American whose father is stationed in England, recieves her Hogwarts letter and goes through her first year in school. Kit has a lot of Mary Sue-like qualities, but Tapestry makes her into a real and rounded OC. Novel length.
Fading Light (PG) by Lyta Padfoot. During the Blitz, Tom Riddle finds himself entertaining a young girl. I like the ending. One shot.
Fed, Dorge, and the Unwitting Babysitter (PG-13) by Trillian Black. The Weasleys hire a babysitter to take care of their youngest children. Hilarious. One shot.
Flower Children (PG?) by Lasayla. Petunia remembers both of her sisters. Angsty. One shot.
Games of Skill and Chance (PG) by Snowballjane. Snape's last term teaching, after the war is over, and he has to adjust. And then a bunch of kids start a games club in his potions classroom. Redemptive, in a reasonable and non-sappy way. One shot.
George, Don't Do That! (G) by Emily Anne. A slice of the life of a long-suffering Nanny at the magical nursery school. Cute. One shot.
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.
Hogwarts: A Hauntin' (G) by Manraviel. A bartender warns a girl about a haunted castle nearby. Cute. Short one shot.
The Hogwarts Fanfiction Academy (PG) presided over by Meir Brin. Includes insane fangirl crushing. This is very, very meta. Bad fanfiction writers are whisked away to Hogwarts, where they are forced to learn to write correctly. It's the HP version of The Official Fanfiction University of Middle-earth. Novel length. It also has a sequel in the works, called In the Keeping of HFA, a WIP.
If It Hadn't Been For the Owl (PG?) by Seldes Katne. Three youngsters have an unusual introduction to the magical world. Good OCs. One shot.
In the Presence of Angels (PG) by Seldes Katne. An old Jewish woman remembers the man she met in the 1930s named Alastor Moody. Nice premise that's well plotted. One shot.
Inspection, 1982 (PG) by KrisLaughs. The Minister of Magic takes a tour through Azkaban. One shot.
Intrepid (PG-13) by Elizabeth Roz. Includes some het teenage romance. Regulus Black's fifth year at Hogwarts. I like the characterizations in this fic. Novel length WIP.
The Lack of a Letter (G) by azriona. A Muggle-born has to make a decision. Good premise for a fic. One shot.
The Lake At Sunrise (G?) by Ignipes. Professor Kettleburn reads his brother's letters as he walks along the lake. A nice look at a part of the wizarding world we rarely see. One shot.
Love on the Quidditch Pitch (PG) by Tess. This one is definitely borderline, but there's so much other stuff going on that you can happily ignore the slight romance if you like. 1953. The Heidelberg Harriers, "fiercer than a dragon and twice as clever," versus the all-witch Holyhead Harpies, founded in 1203. It was just another Quidditch game... but it became legend. Heck, how could a seven-day game with captains proposing marriage, crazy announcers, dragons, and all sorts of other craziness not? WIP, novel length.
Mad Dogs and Englishmen (PG-13) by bruno. A young Death Eater takes on the task of burying a former colleague. Post-war. One shot.
The Man Who Won November (PG-13) by bruno. There's a little sex, though it's not shippy. A young wizard wins an interesting game of poker. This is an all-around excellent fic and story. Chaptered.
Moondance (PG?) by JiminyC. During Harry's fourth year, Remus finds a young girl who is also a werewolf. Hopeful. Chaptered.
Notes on Session 9,204 of the Committee for the Control of Magical Literature (G?) by Shauna. The Committee of the title comes together to discuss banning a book by a certain Lord Voldemort. Good and messy, with all the shades of grey that that question implies. One shot.
Oblivious (PG-13) by Jess Pallas. Includes a few very small references to sexual activity, but it's overwhelmingly gen. The Order finds out that a feral werewolf has been hired by Voldemort to kill Harry Potter. But what's his connection with Remus Lupin? Interesting plotting and ideas. Novel length WIP.
Once Upon a Time (PG) by Lazy_neutrino. In a rather disturbing future, a wizard tells his son the story of Peter Pettigrew. Well written and subtly horrifying. One shot.
Once Upon A Time, In Egypt (PG-13?) by Josan. Offhand mention of m/m. Bill Weasley tries to convince former Hogwarts professor Severus Snape to come to Egypt and work on a burial dig. It's excellent all around. Long one shot.
The River Child (PG-13?) by Ignipes. Remus visits Japan and learns about kappas. Creepy. One shot.
Running Close to the Ground (PG-13) by After the Rain. Includes some het. Peter Pettigrew and the rest of the Death Eaters' Drinking and Cynicism Society as the war comes to an end. Wonderful characterization and plotting. Novel length fic.
The Secret Language of Cats (PG) by thistlerose. Remus meets his great-grandmother. This is an absolutely beautiful fic. One shot.
Selfinsertion O'Bugger Subtlety and the Philosopher's Stone (G) by Nights Mistress. Self is an 11-year-old member of the IRA who comes to Hogwarts and plots to blow it up along with his fellow members of House Hufflepuff. Very funny and subversive. Novel length WIP.
Sin of Lycaos (M) and its sequel Wolf by Ears (M) by D.M.P. The first fic includes a little flirting, as well as a sexual assault which doesn't get very far; the second one is definitely borderline. What Lupin was doing during the GOF year, with a lot of werewolf rights stuff thrown in. AU. Both novel length; sequel is a WIP.
Sixteen (PG-13) by MMM. There's some failed flirtation. Snape's life the summer and fall after the Pensieve events. Plotty. Novel length WIP.
The Smallest Slytherin, An Obedient House, and Salazar's Orphans (probably PG-13/R) by Rebecca Webb. Snape seems to be the ladies' man of Hogsmeade *raises an eyebrow*, and there's various non-serious teen romances. This chronicles the adventures of an OFC, Violet Guilford, who's sorted into Slytherin House during Harry's fifth year. (It's not OotP-compliant.) Her Snape strikes me as the way Snape might be about five years after he came to terms with the whole Marauders thing, and I don't see Dumbledore letting him cane his House. Violet rather toes the Sue line at times, though she usually gets called on her behavior. Having said all that, I rather like these stories. If nothing else, there are so many fun little touches -- the cup game, McGonagall and Snape's rivalry, Floo Tag. Rebecca's writing rather improves as the series goes on; for that reason, and perhaps because it focuses more on canon characters, I like the second fic better than the first. Three novel length fics; the third is a WIP.
So You Want To Go To Hogwarts? (PG-13) by Hijja. It starts out light-hearted, and gets progressively darker and creepier. The narrator has taken a good strong look at the Wizarding World, and she's not sure she likes what she's seen. One shot.
The Staff of Orkney (PG-13) by Ms. Snape. Professor Severus Snape's cousin, Salazar, comes to teach Defence at Hogwarts. He also carries the Staff of Orkney, a magical device with great powers. Ms. Snape does a good job of giving this OMC a well rounded character, and the plot isn't half bad either. Novel length.
Still One Left (PG-13) by Mortalus. There's a teeny allusion to romance in the last chapter. When Severus Snape is wounded near death, his brother, the Seneschal of Europe, comes to his bedside. Angsty, but with a satisfactory resolution. Not OotP-compliant. Novel length.
Take Up Serpents (PG-13) by Mariner. Tom Riddle travels to America to apprentice to a wizard. One shot.
That's What Friends Are For (PG) by Dien Alcyone. The new Defence professor shows up. And he happens to be friends with Snape. (Pause for shock/gasp/horror.) A nice little story. WIP, most likely abandoned.
They Shook Hands (PG) by Dethryl. It's fairly obvious how the kids will pair off when they get older, but for now it's pure gen. This is another AU, this one asking what would have happened if Draco had befriended Harry in Madam Malkin's instead of putting him off. As a result, Harry is sorted into Slytherin, and everything changes. I like the OCs in this fic. Novel length, WIP. It's now at the beginning of Harry's second year.
Thine Own Self (PG-13) by Perri Smith. The Muggle-borns in Slytherin house are rapidly running out of options, and Dumbledore still isn't back. MWPP-era, with wonderful, believeable OCs. Chaptered fic.
Things That Don't Exist (PG-13) by shadoed. A Muggle notices a striking girl in the library. Short one shot.
Transmit and Recieve (PG) by Kay Taylor. Draco's Mudblood cousin (not Tonks) visited the manor once. Angsty. One shot.
Twisted Loyalty (R) by Ayla Pascal. The story of a Hufflepuff who became a Death Eater. Creepy, with a memorable OC. One shot.
Two Hundred Sixteen (PG-13) by Telepwen. People die in war. Everyone knows that. Thoughtful. One shot.
Uric the Oddball and the Wild Hunt (PG) by Ariana Deralte. It's 1680 and Uric "the Oddball" Beaufolle is starting at Hogwarts. New teachers. New students. New problems. Just how much trouble can an eleven-year old get into? Plenty. Uric is absolutely awesome. Novel length.
The Warden (PG-13?) by Rilina. Bellatrix's imprisonment in Azkaban, told from the POV of the prison's warden. Wonderful characterization of Bellatrix, Sirius, and Barty Crouch, and the warden is a great OC. One shot.
Water-horse (R?) by Igenlode Wordsmith. Snape comes into possession of a kelpie and decides to harvest its blood, with not so good results. Scary, and it doesn't end well either. Novel length fic. You probably shouldn't access this page without your pop-up blocker set.
The Way of the Wolf (G) by Wahlee. The first full moon after the events of OotP, Remus has a chat with a wolf. Eddings readers will recognize the patterns of speech. Angsty, but ends on a hopeful note. One shot.
Winter's Debt (PG-13) by La Guera. Includes references to sex, though it's not shippy. Draco Malfoy remembers what he lost in the War. Gorgeous, gorgeous story. One shot.
The Wizard From Outer Space (Meta Remix) (PG) by AJ Hall. This is a remix of a drabble written by Halrloprillalar which is quoted in its entirety at the beginning of the fic. Arthur Weasley stumbles into a con. Written from the POV of one of the fen, it's quite reflective. One shot.