May have been accidental, but during Mark Millar's arcs, there is one where The Invisible Woman, along with a lot of other super heroes from the year 25xx, goes back in time to bring their civilians into the old Earth. To do this, they have to use Galactus as a battery. The fight brings the number of living heroes from hundreds to six. The Invisible Woman remarks that her 'Husband and children died to get there.' It was strange when she didn't mention Johnny, who was standing right there. Then I realized that was because, since they were from the future, Johnny was already dead. It was foreshadowing his death a good twenty issues before the it ever happened.
Probably just a coincidence, since Johnny returned from the dead 12 issues after he died in the first place.
In an issue of Mark Waid and Mike Wierango's run, the Fantastic Four basically meet God — who turns out to be a comic book artist with an unseen collaborator who bears a striking resemblance to Jack Kirby. Which is not only a perfect tribute, but makes complete sense on a metaphysical level; who else would a comic book superhero view as God but the artist / writer who created them and the world they live in?
I always used to think Mister Fantastic was a dumb superhero name, mainly because it's so non-descriptive of his powers. Then it hit me; this comic came out in the era that gave us the expression "Plastic Fantastic". So, it's basically a somewhat subtle way of saying "Yeah, he's basically our answer to Plastic Man." —Cuchulainn
Reed Richards Is Useless actually makes sense considering that most of the comics came out during the Cold War - in fact, if we apply comic book time to the Marvel Universe from the Fantastic Four's debut onwards, they're STILL in the Cold War. So let's say that Reed decides to release the Universal Translator to the public, or to the military? Suddenly, it becomes much easier to translate Soviet communications. What if the USSR replicates this technology? Then both sides of a nuclear standoff can spy on each other without needing a translator - and the same technology could be repurposed to hack any computer. How long until a nuclear war breaks out in that situation?
The early comics have a lot of this, due both to Values Dissonance and just bad writing. For example, the treatment of the Skrull agents in #2. Instead of imprisoning or executing them, Reed literally turned them into cows. This was (and still is, much of the time) treated as funny for the absurdity of it, but is actually really horrible if you stop to think about it. Imagine if that had been done to a human villain...
Throughout the first season of the 1990's Fantastic Four cartoon, one of the supporting characters was the Baxter Building's landlady who also lived there. Then in the second season's first episode the Baxter Building gets destroyed, and she's never seen again. Was she still inside during the destruction?
Before they go in to stop Doom, Johnny clearly states that the building had been cleared out.