The Amazing Spider-Man #268 - September, 1985

Though G.I. Joe was usually considered separate from the rest of the Marvel Comics universe, the Joes did manage to sneak into it during "Secret Wars II", a multiple-series crossover including nearly all of Marvel's superheroes. This issue of The Amazing Spider-Man includes a Army unit led by a sergeant who looks remarkably like Duke, though he and the Joes are never referred to by name. Click the below for scans of two pages from the comic, courtesy of "Zartan" from the Devil's Due web site message boards:

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G.I. Jack Rabbits - December, 1986

Released by independant publisher Excalibur Publications, G.I. Jack Rabbits was an obvious spoof of G.I. Joe. It's cover parodied the cover of G.I. Joe #1, right down to the logo. A second issue was planned for February of 1987.

Scans of some of the issue's character dossiers and a larger image of the cover can be found at YoJoe.com.

Boris the Bear #9 - April, 1987

Dark Horse Comics' Boris the Bear often parodied other comic books and one of them was G.I. Joe. The ninth issue of the series had a cover based on the cover from G.I. Joe #53, complete with Boris dressed as Snake-Eyes and many more Joe look-alikes around the border.

Click here for a larger image of the cover and other details from Dark Horse's official web site.

Deadpool #42 - May, 2000

This comic issue parodied G.I. JOE #21 -- "Silent Interlude" -- in both cover, story and even title ("Silent, But Deadly Interlude"). On the cover, Deadpool (named "A Real American Zero") recreates Snake-Eyes' pose, and inside, the story is for the most part, silent.