The Fantastic Four vs. The X-Men limited series is a perfect example. Though the first issues's cover matches a dream sequence, issue 2's cover shows Mr. Fantastic murdered by Wolverine (not in the story), issue 3's cover shows X-Men attacking the FF while wearing Doom's masks (never happens) and issue 4's cover shows the X-Men impaled corpses, the FF rising like zombies and Dr. Doom cowering in fear or Franklyn Richards (as you might have guessed, nothing even remotely close happens in this issue). Wanna know the most bafling part? The covers were drawn by the same people who did the interior art!
The Emma Frost series was a cute teen drama about a younger version of the title character pitched at a mostly female demographic. This was undermined because the covers were pieces of absurd fanservice featuring the adult Emma in a costume even skimpier◊ than the one she usually wore in New X-Men - and if you're familiar with that title, you know that's not an easy bar to reach. (Warning, NSFW.)
Check out Superdickery.com for dozens of examples of dishonest Superman (and other) covers. For that matter, check out the entire site, as it rocks. (Though it will suck out hours of your life you'll never have back... just like TV Tropes).
A late 80s issue of Superman lampshaded this with Mr. Mxyzptlk indicating that the cover, a giant sized Superman destroying skyscrapers, probably wouldn't actually happen.
Something of a running gag among comics fans is how many covers Wolverine has appeared on for comics in which he wasn't even mentioned secondhand.
The trope was acknowledged in the nostalgic comic-oriented novel The Amazing Adventures of Kavalier & Clay, when a character finds the latest issue of The Escapist has a cover in which the eponymous hero is being executed by his own alter ego; the character is mildly intrigued but knows that the event will likely turn out to be a dream or an alternate reality or some other cheap trick, if it in fact appears in the issue at all. That may have been directly inspired by the Silver Age Superman cover that had Superman stand around mocking Clark Kent as Kent got beaten up. As it turned out, this was just a metaphor for the fact that Kent had given up being Superman.
The cover of Amazing Spider-Man #75 is "Death Without Warning" and shows Spider-Man mourning over a dead body. Nothing like that happens in the comic. What's more nobody in the story dies at all. Although to be fair, one villain does get de-aged seemingly into nothingness, so it did appear that he was dead.
The very first issue of Captain America Comics shows CA punching out Adolf Hitler. Hitler doesn't appear in the comic (although various other Nazis do, including the Red Skull).
The cover of Uncanny X-Men #244 showed Dazzler, Psylocke, Rogue, and Storm cowering in terror from a foe they called "the M-Squad". In the actual story, the M-Squad was a bunch of complete losers who fancied themselves mutant hunters, who the X-Ladies came across trying to apprehend a young mutant while they were shopping at a mall; the heroines pretty much trounced them good. (The cover was likely a joke.) Still, the issue was rather significant due to who the "young mutant" in question was; Jubilee, making her debut in this issue.
Archie Comics usually just display a single gag panel which has nothing to do with any of the stories within. A glaring example of this trope, however, is one for the Betty and Veronica Double Digest issue 128. On the cover, there is a picture of a phone being held by one of the girls, and you can see an image of Archie and Cheryl Blossom in the same image. There's a subtext on the side of this cover that says "Cheryl's back... look out 4 Trbl!" implying that this is the opening story. Not one single story in that book contains anything regarding Cheryl.
The Marvel issue of "What If?..." that dealt with the Fallen Son storyline had a cover of Captain America carrying an apparently dead Iron Man in a dramatically mourning way. The contents of the comic... weren't nearly so touching.
Many issues of What If...? have covers that pose more dramatic questions than the ones actually addressed in the issue, and often emphasize fairly minor parts of the story. Take, for instance, vol. 2 #5, "What If The Vision had Destroyed the Avengers?" The Vision's role in the story is rather limited — the issue is really about what would have happened if Wonder Man had survived his first encounter with the Avengers.
Vol. 1 #39, "What If Thor battled Conan?" is the question asked on the cover, which depicts Thor and Conan in aggressive stances with weapons raised at each other. Inside, the title page instead asks "What if Thor of Asgard had met Conan the Barbarian?", and the two fight only briefly before becoming the best of friends.
The cover of What if: Avengers vs. X-Men #2 features Thor, Vision, Nova, Ms. Marvel, and Black Panther becoming an alternate variation of the Phoenix 5. In the actual comic, the Phoenix force attacks Thor, and only possesses Nova, Ms. Marvel, and Vision for a few seconds before abandoning them to turn Hope Summers into the Dark Phoenix.
The cover of one old Star Trek: The Next Generation comic shows Captain Picard floating around in a space suit with half of his face covered in green slime and Counselor Troi looking-on in horror and disgust. Nothing even remotely similar happens at any point in the issue; no space suits, no green slime, and Counselor Troi is barely even featured.
Most World War II era Marvel Comics have Captain America, Human Torch, and Sub-Mariner having epic battles against the Axis on the cover. The stories themselves though have none of those and are usually about Those Wacky Nazis having their plans for world domination foiled by the heroes.
Malibu Comics used to have a major villain named Rafferty, whose gimmick was that he came with an editorial promise: every time he appeared, a superhero would die! This led to a slew of issues featuring him, many of which showed him threatening a major character on the cover. Too bad those were hardly ever the characters he actually killed. In fact, in most cases he just killed a random walk-on character who had been created just so Rafferty could off him.
Atomic Comics quickly grew guilty of this. While Madman comics had started out having actual, if bizarre superheroic adventures, his latest series, Atomic Comics was much more philosophical than anything else. However, from looking at most of the covers, you would not know this. For example, one cover had two girls, his girlfriend Joe and his friend Luna, who had been fused into the same body in-comic, fighting over him and trying to pull him away from the other, much to his dismay. In the actual comic, the two are complete at peace with each other, only Joe has feelings for Madman, and in fact, the issue isn't even centred around this.
Issue #238 depicted Sonic fighting Mecha Sally, Tails whipping Drago, and Amy about to cave Eggman's face in with her hammer. In actuality, Tails is the one who fights Sally (briefly), Drago is beaten into submission by some wolves, and Eggman doesn't even enter the battlefield.
Amy is featured solo on #240's cover, yet she only appears on the first page. Wouldn't it have made more sense to feature Rotor and Silver instead, since they actually have major roles here?
Further back, #175 showed Eggman holding Sonic in chains, even though Sonic is actually one of the few to escape the destruction of Knothole and imprisonment in the egg grapes.
#225 features the entire Freedom Fighter group, even though only Sonic and Sally have anything more than a cameo within the issue. Most egregious is Rotor, who is given a prominent position on the cover despite not appearing in the issue at all.
All three of the Freedom Fighter teams are crammed together for a group shot on #241's cover, implying some kind of massive team-up. Too bad - the issue is actually about Naugus and Geoffrey arguing over politics and morality, while Sonic and Rotor's teams make pointless cameos. (Silver's team doesn't appear at all. Go figure.)
The main cover Sonic Universe issue 56 features Amy Rose, Blaze The Cat, Marine The Raccoon, Cream The Rabbit and Cheese is a boiling hot cauldron being cooked for Captain Metal's pleasure but in the comic it self that does not happen.
The main cover of Sonic Universe issue 57 features Amy Rose, Blaze The Cat, Marine The Raccoon, Cream The Rabbit, Cheese, Bean and Bark fighting over the Red Soul Emerald underwater while a giant squid attacks them. The giant squid attacks the characters toward the end of the issue but the fighting underwater part does not happen inside the itself at all.
The solicited cover for The Avengers (vol. 4) #19 showed The Vision from Young Avengers as part of the new team that was being assembled in the wake of Fear Itself. When the actual issue itself dropped, the cover had been changed to show the original Vision in place of his successor. The ruse was meant to both hide the fact that Brian Bendis was resurrecting the original Vision in that issue, and that the teen Vision was slated to be killed off in the finale of The Children's Crusade.
The last issue of the old Chip 'n Dale Rescue Rangers comic book has a cover depicting Chip, Dale, and Monterey Jack fencing with a one-eyed mouse who has apparently taken Gadget hostage, and it is given the caption "His name is Ransom - and he means trouble!" Not only does this scene never happen in the issue itself, but Ransom isn't even a bad guy.
The Muppet Show Comic Book: The Treasure of Peg-Leg Wilson has two. The most egregious since it's used for the cover of the TPB is Peg-Leg Wilson in a ghost-like form laughing maniacally while the cast looks on in shock and horror, seeming to imply the story arc is some sort of ghost haunting. Peg-Leg Wilson appears on one page in that issue, and it's just a visual narration since Gonzo is reading about his history. Another cover has Kermit and Kismet the Toad in a face-to-face confrontation. Turns out Kermit hired Kismet for a closing act intended to feature Kermit lookalikes (most of which never showed up), and has absolutely no reason to be mad at him at any point in the series. The weirdest part of these examples is that the writer/artist of the series also does the cover art.
The cover for the JLA story Justice For All depicts Superman and Captain Marvel fighting while the Justice League and Justice Society look on in horror. In the story itself, the two heroes' "fight" consists of Marvel knocking out Superman with two punches to prevent him from following Marvel into the 5th dimension.
Issue 9 of the post-RebirthGreen Lantern series features Hal Jordan and Batman in the middle of a fight with each other. It's true that Batman does punch Hal in the issue...as a lighthearted revenge for something that happened in an earlier issue. Most of the issue is the exact opposite of the cover, featuring Hal and Batman becoming friends again.
Sal Buscema was fond of this when he was the artist for Spectacular Spider-Man. Once issue had the Rhino squeezing the life out of Spider-Man on the cover with a blurb indicating that Peter was gonna receive A Fate Worse Than Death. In the issue, Spider-Man is infuriated due to the machinations of Harry Osborn, the second Green Goblin and ends up giving Rhino a No-Holds-Barred Beatdown that leaves the villain crying for mercy. Another issue a couple years later show the Green Goblin gloating over the bodies of Spider-Man and the X-Men. While the X-Men did appear in that issue (it was the final chapter of a three-part storyarc about something different), they never fight the Green Goblin. Instead, Harry Osborn simply returns toward the end of the issue, setting the stage for the next arc.
One Spider-Man cover seemed to pull a subversion on itself. The cover had Hydro-Man declaring victory over Spider-Man, but with Venom's face in the corner, grinning, and saying, "Yeah, right!" making it look like the cover was a joke (and that Venom was actually the focus of the story). The truth is, there was a fight with Hydro-Man in the story, Venom did escape from the Vault, but both had little to do with the actual plot, which was a poignant story of character development for Aunt May's beau Nathan Lubensky, who's gambling addiction had gotten him in trouble with some loan sharks. (This addiction turned out to be a Foreshadowing of what would eventually lead to his death at the hands of the Vulture, sadly.)
In the six-part Spider-Man story "The Assassin Nation Plot", one issue had a cover showing Spidey confronting Sabretooth. Sabretooth did appear in the story, but he and Spidey never met; Captain America and Silver Sable fought the villain, while Spidey was hundreds of miles away fighting terrorists. (Word of God claims that Todd McFarlane penciled the cover before the script was finalized, and while he knew Sabretooth would appear, he didn't know in what regard. The cover was kept because the editors liked it so much.)
One Sonic the Comic cover prominently featured Sonic's long-lost brother Tonic standing alongside Amy Rose. In the comic, Amy and Tonic barely interact, and "Tonic" is exposed as Metamorphia (again) within a few pages.
Another cover shows Knuckles and Shortfuse charging into battle with each other. The actual "fight" consists of two blows and the misunderstanding that led to it is quickly cleared up. (As this was a one-shot, there wasn't much time for anything else.)
Both the cover and teaser to Issue 178 proclaim "KNUCKLES VS. CHAOS!!!" With Knuckles and Chaos squaring off. In the actual issue Knuckles jumps to fight Chaos but is instantly crippled by Chaos's fear ability and is left like that for the rest of the issue.
A terrible habit Marvel is getting into these days is releasing variant covers for their comics to promote films. For example, around the time of the movie, many comics started getting variant covers with The Mighty Thor or his supporting cast doing something completely unrelated to the issue. Made funnier (and more obvious) with any covers involving Loki, since he's about 10-13 years old physically (it's Depending on the Artist) right now. You see a grown-up Tom Hiddleson Loki? It has nothing to do with the story.
The covers to Batman and Robin 23-25 all show Jason Todd in the Red Hood costume he wore during Grant Morrison's run. The problem however is that Jason never wears it, in fact he dons a new costume at the end of the second issue. Which makes the third cover◊ seem like a Take That in hindsight.
Another issue's cover has Giant Man displayed, despite him not appearing in either of the comics within.
Fans of comic book bondage refer to these as "'gotcha' covers" because they display a woman Bound and Gagged or in some other type of peril that doesn't appear in the comic itself.
The cover of the first Impossible Man Summer Vacation Spectacular (from 1990) shows Impy sunning himself on the beach with almost every major hero in Marvel buried to the neck in the sand around him, with Doctor Doom looming over him. Impy quips, "Like I told these other bozos, quit blocking my sun!" implying he had beaten up the other heroes. It was done for laughs, of course, but there was nothing similar inside the comic. (Which was many different stories about him playing pranks on various Marvel characters.)
Sometimes covers for "big" story lines tend to exaggerate just how many people are involved. Such as in the book "Batman: Battle for the Cowl", it showed characters such as Batwoman on the cover even though she was neither seen or mentioned at all in the storyline.
A common trick in superhero comics is for the cover to feature the villain(s) standing on top of the hero's dead or unconscious body. This rarely happens within the book itself, or if it does, the hero recovers and beats the villain down anyway.
The cover of Victorian Undead: Sherlock Holmes vs. Zombies depicts Holmes as a zombie smoking his pipe. He is never turned into a zombie at any point in the comic. Also he is shown in his stereotypical deerstalker hat, which he never wears in the story at any point.
With the Swamp Thing ongoing series beginning in 2011, the first four covers depict the titular Swamp Thing. The only problem is that, for the first several issues of that run, Alec Holland wasn't even the Swamp Thing. It's only later that he actually changes into the Swamp Thing. The covers depict events that, while vaguely related to the contents of the issue, are horribly inaccurate.
Most modern comic books have different artists for the cover and for the comic book itself. The cover may not lie about the content, but about the style. You may buy a comic book with a magnificent cover and find that the interior art is drawn by a different artist, with a completely different style.
Spider-Man 694 features the end of a story arc involving 'Alpha' a teenager imbued with potentially the strongest powers in the Marvel Universe thanks to an experiment by Peter gone awry. As well as these powers, he's also become a selfish jackass, causing Peter to try and remove his powers before something bad happens. The cover of course features Spidey and Alpha high in the air, ready to beat the other into a pulp, with the words 'Battle Of The Half Century' hovering over them. The actual book? Well, they and the Avengers fight Terminus, but not a single punch is thrown between Alpha and Spidey; there isn't even a shouting match for them to exaggerate.
One of the Spider-Man graphic novels, the one collecting the Ends of the Earth storyline, does this in a relatively minor way. It should be obvious that Ock isn't actually going to fight Spidey in open space above the Earth and that that's just a cool cover, but Spidey is seen on the cover in his classic garb, when he spends 90% of the book in his new Spidey-armor, and only wears his classic outfit in the first book in the collection (and it's not used to fight Ock).
Shortly after the Batmobile was introduced in the comics (Detective #362) following the Adam West movie and TV series, (the first of which looked nothing like the Lincoln Futura Batmobile), it slowly started to resemble◊ the Futura more and more (Detective #371 and #375, though later issues change it to look like a Jaguar E-Type), the cover of Detective #375 has Robin drving the Batmobile and Batman waving to a crowd. The Batmobile does not appear in that issue.
In Death Of The Family, one cover shows Harley Quinn and Joker going back to their abusive relationship. However, it turns out that there is nothing romantic between them, and Joker tries to kill her off as well as revealing that she's just part of a long chain of Harley Quinns that he has killed off at one or another. She escapes him and lets herself be put into prison.
An interesting subversion occurs on the cover of Love and Capes: What to Expect #5. In the story the Crusader (Mark Spencer) and his pregnant wife Abby switch bodies, but on the cover they don't switch bodies but just the suits (and now Mark has the "baby-belly") in order to convey what happens without words.
On the cover for Marvel Comics's Our Love Story #24 depicting the story "Joe Howard's Chick", protagonist Connie Smith doesn't appear to notice the boy approaching her and being stopped by another boy. Her noticing this is the turning point of the story. Compare the cover◊ to the actual scene◊.
If you've never read Garth Ennis' Preacher, the cover of the first issue can easily fool you into thinking that the hero, Reverend Jesse Custer, is the primary antagonist of the series (or at least a Villain Protagonist) even though he's one of the most sympathetic protagonists that you're likely to find in a Vertigo Comics book. How misleading is it? See for yourself: it's currently the page image for Sinister Minister, a trope that Jesse is emphatically not an example of.
The cover of the BIONICLE comic To Trap a Tahnok shows a Tahnok stealing Tahu's Golden Mask and another placing a mind-controlling Krana on his face. No event like this ever happens in the comics or books. One panel does show a random Lehvak Va carrying Tahu's mask, but when Tahu himself shows up in later, he has his mask on as if nothing had happened. The writer later explained that his losing and regaining his mask happened between scenes.
The 19th issue of Batman spinoff Batwing features the titular hero crawling on the ground, badly wounded and desperately trying to get away from a sinister looking Batman. The cover headline even read "A HERO FALLS..." This seemed like a big deal, since DC had already announced that David Zavimbe would be replaced in that issue by a new hero who would inherit the name of Batwing. The implication on the cover was that David would die, and that Batman was somehow responsible. In the issue itself, David simply decides to retire, and Batman is nothing but supportive.
Most of the revealed covers for My Little Pony: Friendship Is Magic (IDW) are sort of just generic "ponies being cute/cool" and very few so far even hint at the return of changelings. Not that we don't expect ponies being cute/cool or anything, but Rainbow Dash doesn't go snowboarding or dressing up as a superhero in Issue #1.
Covers for The Frankenstein Monster would often depict women in peril, when none in the story is not in peril at all. However, the most misleading cover goes to issue 15, which depicts several Night/Clone-Creatures surrounding the Monster, while the one and only is featured in the story.
One issue of Joss Whedon's run on Runaways had a variant cover featuring zombified versions of Gert Yorkes and Alex Wilder. Only Gert appears at any point in the arc, and only as a hologram.
The cover of Avengers Academy #31 (published during the "A vs. X" event) featured several of the younger X-Men, like Dust and Surge, being delivered handcuffed and collared into an area surrounded by a chain-link fence topped with barbed wire. In the issue itself, they're dropped off at Avengers Academy by Wolverine, who's seeking to keep them safe from the fight between the X-Men and the Avengers. None of the kids are particularly happy about it, but they're never put in restraints.
Comic Book/Quasar #29. The cover depicted Quasar as pregnant, parodying the famous Demi Moore Vanity Fair cover. In the comic, while the character named Her does begin the process that will eventually make Quasar (and several other male superheroes as well) incubate a child, Quaze is able to talk her into cancelling it before any reproduction even occurs, much less the full-term that the cover showed.
Earth 2 #7 is titled "Flight to the Death!", showing Green Lantern and Hawkgirl fighting hand-to-hand on the cover. In the story, all they have is an argument over Alan not joining the team.