I Wrote Our Story

"I decided. The main character is going to be a samurai."

—Chihaya Ikaruga, Asu no Yoichi

Sometimes, when main characters are writers/animators/mangaka/directors, they write/film/draw a story including the main characters from the actual story. Though this is not a common thing, it's still worth the mention.

Examples of I Wrote Our Story include:

Anime and Manga

As mentioned above, Chihaya's manga is about a samurai. This samurai is surrounded by four girls. Incidentally, Asu no Yoichi is also about a samurai surrounded by four girls.
Toujou from Ichigo 100% writes fantasy novels. At one point, the main character has to choose among some girls. Just as Manaka has to choose.
- Also, the films they make together differ very little from reality.
Episode 00 from The Melancholy of Haruhi Suzumiya
True Tears' main character, Shin'ichiro, is drawing a story about a rooster that tries to fly. This 'flying' aspect is actually the point of the entire anime.
Haruka from Kimi ga Nozomu Eien desperately wanted an image book about saying goodbye. Which is exactly what she does.
The entire premise of one episode of Student Council's Discretion.
In the epilogue of Eyeshield 21, Karin becomes a mangaka, and her editor asks her to use her experience in American Football to write a manga about the sport, with the legendary runningback Eyeshield 21 as the main character.
In Keroro Gunsou, Aki uses Keroro and his friends as the inspiration for her latest manga series.

Secret Window, based on the book by Stephen King, starred Johnny Depp as the psycho writer.
Both the main characters from Throw Momma from the Train do this at the end after the plot is resolved. Billy Crystal's character (the one who is an actual author) is outraged that his former student, played by Danny DeVito, may have beaten him to market with the same story and seems to consider actually murdering the man out of anger, but DeVito's turns out to be a children's book with a family-friendly ending and they end up happy for each other and successful.

Seinfeld. The Show Within the Show is about incidents surrounding the main characters' lives. (I.E: yeah, it's about nothing.)
In Supernatural, a character is chosen to become a prophet of God, and begins having dreams chronicling the adventures of the lead characters. (Basically, he's seeing what the show's audience is seeing.) But, not knowing that his visions are true, he proceeds to write them down as books and publish them under a pen name. Needless to say, he's a bit shocked when he finds out the truth, and is flung headlong into his own world filled with demons and monsters.
- Of course it is later implied that said character is actually God.
The titular character of Bones writes novels about her life as a criminal anthropologist. This is actually Truth in Television - the show is loosely based on the life of Real Life forensic anthropologist Kathy Reichs, who wrote a series of novels based on her life and career.
In the US version of Queer as Folk, Michael and Justin write and illustrate their own comic book, Rage, which features Brian as the lead character and tells stories right out of the characters' own lives.

The Word Weary is written by John Kossler and features a protagonist named John Kossler writing a comic about his life.