Many of the films mentioned, like the 1990 Captain America, 1989 Punisher, and Man-Thing, are direct-to-video, not actual theatrical films.
Of the 41 theatrical feature films based on Marvel Comics, he has appeared in most. 1986's Howard the Duck was done before Marvel Entertainment got on their filmmaking kick, and before they even decided to start giving Lee cameos. That began in 1998 with Blade.
At first, it was determined that Lee would only appear in films based on characters he created. Thus, he does not appear in...
Blade 1, 2, & 3
The Punisher or Punisher: War Zone
Ghost Rider or Ghost Rider: Spirit of Vengeance
Wolverine 1 & 2
He also did not appear in X2 because, at the time, they were only thinking of giving him cameos in the original films. That did not last, and he's appeared in most sequels.
I don't know why he doesn't appear in X-Men: First Class or Days of Future Past, or 2015' Fantastic Four (all Fox releases), but he is in Apocalypse.
Despite not creating Captain America, it at least was a character whose history he was influential in, and he gets a cameo in each Cap movie. Folks have recently decided to start putting him in films of characters he did not create. Hence, he appears in Guardians of the Galaxy and Deadpool.
The films Lee DOES appear in are...
- 2000: X-Men
- 2002: Spider-Man
- 2003: Daredevil & Hulk
- 2004: Spider-Man 2
- 2005: Fantastic Four
- 2006: X-Men: The Last Stand
- 2007: Spider-Man 3 & Fantastic Four: Rise of the Silver Surfer
- 2008: Iron Man & The Incredible Hulk
- 2010: Iron Man 2
- 2011: Thor & Captain America: The First Avenger
- 2012: Marvel's The Avengers & The Amazing Spider-Man
- 2013: Iron Man 3 & Thor: The Dark World
- 2014: Captain America: The Winter Soldier, The Amazing Spider-Man 2 & Guardians of the Galaxy
- 2015: Avengers: Age of Ultron
- 2016: Captain America: Civil War & X-Men: Apocalypse
- 2017: Guardians of the Galaxy Vol. 2, Spider-Man: Homecoming & Thor: Ragnarok