Jan's appearance in Gifts of Wandering Ice. It's foreshadowed on page 175 of the comic (where Rita hesitantly speaks of an outcast who is a shame to her tribe) and Jan himself appears only on page 290.
These twocomics have the characters read a note Tedd's dad left for him. While he reads it normally, each other person who reads it reads something related to the future: Justin, Nanase, Sarah and Tedd
Most of the Sleepy Time storyline was a serious take on it though. All the dreams are this and/or Character Development. Proof? This foreshadows Elliot gaining a superhero spell and This foreshadows Nanase getting into a relationship with Ellen.
What's seen here translated with this. "Death. It Is Time For The End Of Man. This Master of Fire Shall Inherit The Earth. My Very Presence Eats Away At Your Flesh" Other than the two bizarre words in the end, it's pretty creepy.
This arc cover is full of foreshadowing (and one Red Herring). It foreshadows the appearance of Abraham and Nanase's angel form.
This sketchbook comic, from January 2011, where Dan notes that "Catalina and Rhoda have never met in canon, but I do think of them as being connected in a strange way". They meet in October of the same year (with the sketch linked as "Foreshadowing or goofy sketchbook? YOU DECIDE!") and are now a couple.
In Get Medieval strip #731, Sir Gerard says: "I'd return via the Moon if that could avoid it." Guess what, 70 strips later and he's on the Moon.
The party wanders into a cave looking for an item for a Fetch Quest and discover that it's inhabited by a dragon. During the fight, the dragon mentions its mom, who thought it important to study other cultures and thus taught him to speak lizard. Later, the party wizard deduces that the Fetch Quest item they were after must have been brought there by a much older dragon. However, no character (and, surprisingly, not a single fan) thinks anything of it. Until the dragon's mom shows up over 400 strips later bent on bloody revenge.
V's, er, thorough and pragmatic approach to problem-solving is hinted at earlier.
This very same comic mentioning "villians fighting eachother to thin the heard" might be foreshadowing for Nale's ultimate fate.
The IFCC (Inter-Fiend Cooperation Commission) first appears as part of a one-panel joke in #380. They then appear as an important part of the plot in #632 (spoilers).
The police chief of Cliffport jokes that the mayor will put his head on a pike for allowing such a ruckus in his town. Turns out that Nale did the mayor's work for him.
When the different parts of Haley's mind show up in her head, one ("the part that is sick of all this emo crap and wants to get back to comedy") has short hair, and very much resembles her after her Important Haircut some 300 strips later.
This strip — it takes some conscious effort to put a mad science related heart exactly there, and if you're thinking coincidence you might have missed the fact the heart was "hit" twice and the first time Agatha was saying love. Or the piece of heart region clothing Gil loses, as if to expose his heart. Agatha touching a heart with seemingly no fear of being mangled by the combat klank, as some sort of symbol of her touching Gil's exposed heart despite Gil's antics. Gil grabbing Agatha is a distinct foreshadowing of the wedding proposal that comes before she leaves the airship. Plus 15 or so threads of you know what I mean about in the forums if you want more esoteric symbols mad love, or Agatha's love of the mad science involved.
Agatha's comment about her "parents" hating the Heterodyne Boys Stories portraying Punch and Judy as stupid foreshadows the reveal that they themselves are none other than Punch and Judy - they feel insulted.
When a jagermonster claims Agatha smells "really goot" in book one, Gil (and the reader) assume he's just being lecherous and disgusting. It later becomes apparent that jagers can smell that Agatha is a Heterodyne.
It gradually becomes evident to the reader that all of the major events in Narbonic have been planned long in advance. The Little Nemo in Slumberland-inspired Sunday strips, especially, hint in beautiful, complicated, cryptic ways at events to come.
In the middle of the series, Dave is lost in time and twenty years later meets a pre-recorded 'future Dave' who tells him a fundamental piece of information: "remember to fill the swimming pool." Years later near the end of the webcomic, this becomes the thing which saves the lives of Artie and Helen, and completely alters the future.
When Hilda Ramirez and Feddyg meet face-to-face for the first time, he mockingly compliments her as "almost Death Note smart." He then proceeds to kidnap her, keeping her alive just long enough for a very Death Note-like The Plan.
Every one of Robin's shirts has been exactly what she's asked for. although usually not how she meant it.
When Robin changes her mind about her roommate being her girlfriend (while bringing her into existence) she says that she is not friends with her in any way, and we will never know how much easier her life could have been otherwise.
This page has a good bit of foreshadowing in it, but then again it also kind of takes place in the future. It's a quasi jump forward in time referring to and before a redoing of a previous serious of events the readers haven't seen yet. with out time travel.
In this comic King Radical is introduced as "the most radical man in the radical land". Later, it is revealed that there is a radical land.
The Future Trading arc has had elements foreshadowed since October 2009. See here. Alsothese. Notice the hairy octopus?
Toward the beginning of Sam & Fuzzy's "Noosehead" arc, Malcolm says some things that most would dismiss at first as being the ravings of a paranoid nutcase who's been breathing too many fumes, but in fact they reference key elements of the coming arc. A guest comic after the arc's completion calls attention to this.
Calliope and Caliborn sharing a body was so heavily foreshadowed, a sizeable portion of the fanbase was convinced that this wasn't going to be the case because, well, it's Hussie. When it's confirmed that they share a body, the narration lampshades how this isn't a shocking twist at all.
Tina's nickname for Monica foreshadowed the role she played in the fixing of the calendar machine. Monica's response to Phix's riddle did the same.
The very second strip shows Monica receiving an ancient Peruvian doll which Amanda says looks like a voodoo doll of Shelly. In the next strip Amanda grabs the doll's foot, and elsewhere the real Shelly feels it. In isolation this looks like a one-off gag, but actually it's a foreshadowing of all the supernatural shenanigans that would later become the strip's main focus. In the strip after that Monica tells Shelly she makes decisions using a committee in her head but it doesn't have a chairperson - a possible foreshadowing of Tina, who is a literal committee of inner demons sharing one body after its "chairperson" (the original Tina) died.
Way back in October of 1999, we saw Oasis get furious at someone, and shortly afterwards the building she was in went up in a fiery explosion. It wasn't until June of 2009, over nine years and 3000 strips later, that we found out that, when Oasis gets mad, she can start fires with her mind. There was loads of other foreshadowing between those two strips, but, if the strip's official forum is anything to go by, that revelation was still entirely unanticipated by the readership.
When Schlock, the Big Bad, expresses guilt at getting "those kids" entangled in his plans for Oasis, Kusari, his greatest assassin, asks if he is referring to the Torg, Zoe, Riff, and herself, which he confirms. She is eventually revealed to have been The Mole in the gang in her false identity as "Sasha".
Miho, her identity, her nature, and her relationship with the boys:
Early on, one of the sketches in the book Piro lost has the same ribbon as Miho, foreshadowing the fact that he's seen her before.
Shortly after the sketchbook example, Miho recognizes Piro's name, despite never being told. She also continues to speak to him in an overly familiar tone before he even knows her name. She was actually close friends with both him and Largo in the Endgames MMO; her character and Piro's even became lovers, a relationship that extended into cybersex.
When pulling Ping out of the arcade, Largo recognizes Miho's tactics, though he can't remember from where. Shortly after, he has a flashback to a fight in a fantasy world with a man with Miho's hairstyle, and tries to tell Piro about it (too bad he wasn't listening). It was Endgames, a unique fantasy MMO that he and Piro played. "Moh" was their friend and ally, until he destroyed the game world. And Largo is right, he was Miho.
In the arcade strip, she muses that she knows both of them, but apparently never met in person before. Again, Endgames.
After bringing Ping back, Miho mentions that "maybe we can all play again sometime." Piro misses the most important part of that phrase (the "again") to wonder if Ping has a multiplayer mode. More Endgames.
Ed and Dom freak out when they see her (Ed's threat detector goes crazy), even more so than when they ran into Junpei. Dom even mentions "That stance...I've seen it before." This hints at the fact that as a badass weapons-grade retired idol, the government treats her as a walking nuke.
The fact that she constantly gives Kimiko advice on voice acting is a clear hint that she was one herself.
When she talks down one of Erika's fans, Largo is in awe of her "raw power." It seems like Largo just being crazy, but idols like Kimiko really are valued for their ability to do that sort of thing.
In Schlock Mercenary, the aquatic, tentacled Schuul being behind the civil war plot is hinted at by the personality-overwriting "hack" being used: this strip shows the hack as water, when its previous use had manifested as someone "moving in", and this one has an interesting shape while melting.
Before Anpu is introduced, the story focuses on a moment on Anubis' mural in the museum.
If you know what ba looks like, you can guess what Anpu does to Edith before he tells her.
It remains to be seen whether it's just a Red Herring or not, but it's heavily hinted that "Anpu" is, in fact, Set pretending to be his fellow deity. Among the hints: red glow of his magic, ambiguous shape of supposed fennec fox, the fact that his tail has two prongs sometimes (a mark of Set's Animal), Heru's animosity towards him and of course the red image of Set's Animal adorning webcomic's page's banner.
Diamond in the Rough (Aladdin), which starts out with seemingly unknown protagonists, throws in clues to who they might be through the character's clothes and items, such as a staff with the head of a bird, or a patterned purple cloak, or a breastplate with a roaring tiger.
Mario & Luigi: Cleanup Crew: Luigi and Mario briefly appear in the beginning of "A Mess in the Making", but the bulk of the chapter is Toad's recollection of the events leading to the current crisis.
In Rain, Maria's comments here and here make a lot more sense when you learn that Emily is pansexual and used to date Maria.
Angel Moxie: When the second seal is broken, non-magical entities are affected by time slowing down. At this point Alex is the only awakened magical girl, so Miya can't figure out why her "normal friend" Riley is unaffected.