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Where: Star Kid (movie)
Comics: Midknight Warrior
Creator: ?
Company: Impulse Comics
In Star Kid the lead character is a fan of the comic Midknight Warrior:
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Where: Smallville (TV series)
Comics: Warrior Angel, Fantasy Comics Featuring Warrior Angel
Creator: ?
Company: Fantasy Comics
Since it would make little sense to have DC Comics within a DC series and they'd want to avoid showing rival companies' comics, Smallville featured the fictional comic Warrior Angel across multiple episodes, showing too many issue covers for me to include them all here.
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Where: Tremors 3 (movie)
Comics: Graboids, Shreikers (sic), Graboids vs Shreikers
Creator: ?
Company: Dark Horse Comics
Produced by Dark Horse Comics as props (and sadly not real tie-in comics) for the movie Tremors 3.
Graboids cover art:
Shreikers cover art:
Graboids vs Shreikers cover art:
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Where: Fringe (TV series)
Comics: Crisis on Infinite Earths, Superman: The Man of Steel Returns, Red Lantern co-starring Red Arrow, Batman, Justice League
Creators: Presumably the same as in our universe
Company: DC Comics
You might reasonably be thinking "hang on, most of these comics exist. Why list them as comics that don't exist?" And that's because while these are real titles for the most part (Red Lantern notwithstanding), these are the parallel universe versions from the TV show Fringe, in a timeline where things went a little differently both in the real world and the comics...
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Where: Back to the Future (movie)
Comic: Tales from Space
Creators: ?
Company: EC Comics
Appearing in Power Rangers Zeo:
While one of Biff Tannen's gang was seen reading the real world Headline Comics in the movie Back to the Future, the SF comic that farmer's son Sherman Peabody was reading was entirely fictional. That hasn't stopped replicas being made and sold, using stories from other weird tales comics, and the comic has since turned up in Power Rangers Zeo, Third Rock from the Sun and Heroes (1st season episode Better Halves), arguably providing cross-reality linkage between these fictional universes.
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Where: Hellboy (movie)
Comic: Hellboy
Creators: Mike Mignola
Company: Dark Horse Comics
Another case of "but this comic does exist!" Yep, the title does, but not this issue, which was created purely to be an in-universe version of the comic in del Toro's 2004 Hellboy movie.
Online!
I just found this link to the various images of the fake X-Men comics in Logan. Notice that the comics call the publisher X-Men Comics Group and the one indicida seen calls it X-men Comics Corp.
https://www.theverge.com/2017/3/6/14821492/logan-x-men-comic-books-wolverine