Aquaman: This happened to the new Aqualad in Young Justice (2010) - the version for the animated series was created first, but his comic-book counterpart first appeared in June 2010. The series premiered January 2011.
New 52: Arthur Light initially appears as an A.R.G.U.S. scientist in Justice League, and doesn't acquire his Dr. Light powers until the Trinity War crossover that kicks off Forever Evil (2013).
Superboy: The villain Black Zero was first seen in a Hypertime window in The Kingdom, a month before his proper introduction on the pages of Superboy Vol. 4. The brief, unremarked-upon image of him in The Kingdom became the cover of the third issue for Superboy's "Hyper-Tension" arc, a semi-sequel to the former.
Marvel really seems to love doing this with video games. They debuted the new Spider-Woman costume in the Spider-Man Unlimited mobile game before officially bringing it into the comics. A few months later, they confirmed that Spider-Man and Spider-Man 2099's new costumes from All-New, All-Different Marvel will be showing up there before officially debuting it in the comics.
Kamala Khan, the newest Ms. Marvel, made a brief cameo in the final issue of Captain Marvel before making her proper debut a few months later.
The Inventor's name is mentioned by Kamala in All-New Marvel NOW! Point One after she destroys a giant junk creature of his creation. Since this story takes place after Kamala has become Ms. Marvel, it's implied that she has already faced him in the past.
In Web of Spider-Man #18, Peter is shoved into the train tracks by a person that did not trigger his spider-sense. This is Eddie Brock, a.k.a, Venom, who would be introduced on-panel in 1988 with The Amazing Spider-Man (1963) #299. Both titles were written by David Michelinie, Venom's creator.
One of the scientists working for Norman Osborn in the first arc is Otto Octavius. He will be important later on, but now, he's just a scientist among all the others.
The police outside the warehouse with the thief that killed uncle Ben were led by Captain Stacy. He will appear as a full character later on, as well as his daughter Gwen.
Kingpin was mentioned in the Bugle, as a story that Ben Urich is working on. He would meet him in the next arc.
Loki first appears in a background shot during the first issue of Ultimates 2, when he's making Thor look crazy.
Hawkeye appears first in issue #7, but he's so tiny and in the background that it would have been easy to miss him.
The Unbelievable Gwenpool: Gwenpool first appeared on the cover of Deadpool's Secret Secret Wars #2.
Other
Heroes: In the graphic novels, Sparrow Redhouse makes a brief cameo in a season one issue, about two years before her proper debut in the "Rebellion" story arc (which also retconned an unnamed, masked extra from the TV series as being her).
Saga: A couple examples show that Brian K. Vaughan does his plotting far in advance.
Yuma is formally introduced after Alana goes to work for the Circuit, but she was first shown as a portrait on the wall in Heist's house (since she's his ex-wife).
The March first shows up on a video call to Freelancer HQ complaining about getting shorted on a job. S/he (it?) appears to attack the heroes in the war for Phang dozens of issues later.
Star Wars Expanded Universe: In the third issue of The Rise of Kylo Ren, a holocron recording of a long-dead female Jedi is shown. Her name is Avar Kriss, and she turned out to be one of the main characters of the then-unrevealed The High Republic multimedia project.
The Tick: Arthur is properly introduced in issue four, but is visible flying around in background shots before then.
Transformers: The Protectobots, Aerialbots, Stunticons, and Combaticons in the MarvelTransformers Generation 1 comic first appeared in Buster Witwiky's dream in a UK filler story before their proper debut in the US comic.
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