Yes, he has.
Stan Lee hasn't just made cameo appearances in comic books - he is actually a character within the Marvel Comics continuity, according to this page on the Marvel wiki.
From the character's History section:
Stan Lee and his then comic collaborator Jack Kirby originally had an agreement with the Fantastic Four that the team would share their adventures with them so that Lee and Kirby could publish factual accounts in their comics. Doctor Doom, setting a trap for Mister Fantastic, forced Kirby and Lee to call Mister Fantastic to their studio to work out a new plot with them. As soon as Doom left with his prisoner, Lee and Kirby warned the other members of the Fantastic Four - which was also a part of Doom's scheme.
Lee and Kirby were refused entrance to the wedding of Reed Richards and Susan Storm. Although he threatened legal action, he apparently reconciled with the team.
Lee also happened to be at the window at one point in time to see and greet a balancing Daredevil. He regretted that Gene Colan was not there to see him too.
Stan, now with moustache and goatee, went to the theater with wife Joan in NYC. The play was not of their liking but Stan found it was short enough to go back home and write the following Spider-Man issue. They then met Daredevil, who was running from rampaging Man-Bull and greeted Stan as "fearless leader". Joan was amazed at seeing a superhero.
Stan Lee and Jack Kirby once observed Scott Summers and Jean Grey kissing on Christmas.
George Pérez and Roy Thomas had trouble with an issue of Fantastic Four - as the Fantastic Four themselves were in outer space, they could not report their findings for Pérez and Thomas to report those and, with the deadlines approaching, Joe Sinnott needed their input to write. They asked Lee for a solution and, when consulting visiting luminary Jack Kirby, the latter suggested they make up a story, something they considered but Lee rejected on principle. The office was then assaulted by the Impossible Man, who wanted to appear in a comic-book, but Lee was against this because Impossible Man comics had received bad criticisms in the past. Impossible Man turned violent, and Pérez and Thomas had to protect Lee from damage. Finally, the Fantastic Four forced Lee to reconsider his position and approve an Impossible Man special issue but, as soon as they all left, Lee took down his promise made under duress.
A version of Stan Lee appeared to The Hulk and went through the story of Bruce's dad's death, using a troupe of actors, before disappearing into nothingness. It is unknown how this version came into being or what it truly was. At that time, visions of Stan appeared in other places, including Stan as a driver to explain a story of Daredevil.
Later, a more worldly Stan attended Karen Page's funeral.
He's an old friend of Ben Grimm, both went out along Jack Kirby when the Future Foundation found a temporary cure for Ben's mutation.
History of Stan Lee character, Marvel Wikia
This link contains a list of comics he has appeared in, including issues of;
- Fantastic Four
- New Avengers
- Incredible Hulk
- Amazing Spider-Man
- Iron Man
- Ghost Rider
- Captain America