There are actually quite a few dedicated fanfic writers out there who try and portray Peter in a positive light. I've tried to get a good sample from each of these writers, and then provide a link to more of their stories.
The reason is I simply have not got that many permission requests returned yet.
I also realize three of the four fics here are slash. I'm not just looking for slash, that's just how it stands right now.
Disclaimer: All work here is the product of the author's imagination and is not intended to infringe on the copyright of any person, persons, or corporation. All stories here are the work of the author; however, and should not be used anywhere else without permission
A Fair Fellowship of Young Squires
By: After the Rain
Summery: Sir Cadogan tells the story of King Arthur to a group of first-year boys
Once hurt and alone, Peter finds himself in a seemingly perfect relationship only to discover that not everything is what it seems and a kind mask can hide a monster. Voldemort/Peter
It Never hurts To Try
Peter gets lured into a bet with Sirius that he doesn't think he can win. Remus, however, comes up with a solution. Short fluffy MWPP fic. Remus/Peter
By: Azriona and Talloaks (linked offsite to their FictionAlley page)
They were the original Trio, planning to spend the rest of their lives together. Fate intervened, and one did not get her letter. One tried to keep them together, one tried to keep them apart. And the other turned darker than the rest could have imagined ... all due to the lack of a letter. Had Lily known that Hogwarts would tear her sister away from her, she might never have agreed to go.
Reflections of Truth
By: Jedi Boadicea
An interpretation of what happened to make Peter Pettigrew a traitor.
Ani adds: Along for a night of mischief, Peter his followed by nagging doubts and forced to confront an uncomfortable truth about himself.
What Lies Beneath
By D.M.P Her FictionAlley Fics
MWPP story from Peter's POV. An in-depth look at his personality and beliefs and how it affects the choices he makes
A Simple Truth
Summery: A drabble: Peter discovers a simple truth about being a Death Eater
Summery: A Drabble: Peter has one thing that James will never have.
Peter and The Wolf
Summery: A Drabble: Lupin herds Peter
Summery: A Short Story: Peter is initiated into the inner circle of the Death Eaters, thinking he still has a way out.
By Gilleonnen Her FictionAlley Fics
Sometimes, you can't be forgiven. Sometimes, you can't forget. Peter seeks judgement for his betrayals.
en échange de âme
Summery: A short story that deal with two spells that were cast on Peter the year the Potter died.
Summery: A short drabble exploring Peter's character through three moments which he recalls. James/Peter
Silver and Green
Summery: Peter contemplates loyalty and duty. Peter/Severus
James/Peter Was it ever suspected? Was it ever intended? They loved each other so much... but one would be the death of the other. Betrayal from both parties, one in a fit of drunken rage, brinks torment and heartbreak to the most unlikely of people.
Once Upon a Time
Summery: A story in which Peter plays the hero.
Tears of a Rat
Summery: Peter spends time with Harry on the day he betrays the Potters and tries to explain himself. What will he say?
Shopping in Diagon Alley
Summery: Don't let this fluffy story that involves James, Lily, and a kitten prevent you from reading. There is also an interesting characterization of Peter Pettigrew
Summery: Summer 1980. Two young men meet in a pub in Knockturn Alley. For ten days, their lives are entwined. But when the Dark Mark burns, no one can fight the summons. Peter/Regulus
Summery: Voldemort bitterly contemplates his relationship with Wormtail, realizing just how close they are (not slash)
Crapulam Terriblem Habeo
Summery: Peter dreams of different wants, desires, and situations. MWPP era.
Follow Me, Into the Night
Peter is a traitor who betrayed his friends to Voldemort. But things are often more than they seem and Peter proves to be true Gryffindor. Trelawney's first prophecy.
Peter and The Wolf
Summery: Remus recalls earlier, more innocent days with Peter. (implied Slash)
Thrust and Release
Rating:R for sexual content
Summery: One hour with a prostitute in a seedy hotel gives Voldemort's second in command the sweet release he so desperately needs...
Just Between you and Me
Summery: When Sirius's date dumps him much earlier than anticipated, all he wants to do is have a good sulk in the privacy of the boy's dormitory. How quickly he forgets that there will be one other boy there...one who's there every Friday night. Very mild slash. SB/PP
By: Webba (Story linked offsite to her FA page)
"I'm going to be a good daddy to you, Abigail. People say it can't be done; that I'm too young and immature to know what love really is. They say that your mummy and I made a huge mistake in making you and it's only a matter of time before we fail you. I promise I'm not going to let that happen, Abigail. As God as my witness, I'm going to do right by you and your mum." One Woman, two Men...one a Hero, the other, a Demon. Bound together by the choices they make: The Woman's, a desire to save her family, the Hero's a mistake of passion and the Demon's the ultimate betrayal. Will Harry and Tessa's love be enough to keep their floundering marriage alive or will the Demon destroy their happiness? A story unlike any other...