Anyone who knows anything about any facet of the realm of comic book mythos knows one fact beyond any and all dispute: the Hulk is one of the baddest characters on the block. Most readers may not even remember times when Hulk was defeated. As one of the most recognizable faces in comics, Hulk stands among a very select cast of characters that for all intents and purposes, simply cannot be offed. In fact, one can very easily get squashed like a grape just for daring to try.
However, readers will come across rare instances when a villain (or fellow hero) manages to take down the Hulk. It should be noted that the Hulk has had many incarnations over the years, even alternate reality versions of the character, all with different power, intelligence and mortality levels. So, while it hasn’t happened often, there have been several times Hulk was defeated.
In the Old Man Logan stories Mark Millar and Steve McNiven tell the tale of a reality where the bad guys finally get it together enough to utterly decimate Marvel's heroes. Only the hardiest of the heroes manages to survive, and one of them is Wolverine, who readers already know is…a devout pacifist who refuses to raise a hand in violence at all, much less pop his claws.
Eventually, Logan come face to face with one of his old allies/enemies - you guessed it: the Hulk. Millar's incarnation of the Hulk paints Bruce Banner as evil and past any point of return. The Hulk literally devours Logan, and sits back to digest his meal, but he didn't really account for Wolverine's healing factor. Wolverine emerges from his belly, to dramatic effect.
In What If? World War Hulk, a vengeful Hulk conquers the heroes of Earth and leaves them with only one option: they must try to end him. Tony Stark calls for a tactical energy blast that he hopes will stop the Hulk, even if it destroys all of New York City. The strike fails and months later Vision finds a scarred Bruce Banner digging his own grave among the ruins of Manhattan, eagerly awaiting his passing by radiation poisoning.
Vision convinces Banner to become the Hulk once more so he can help beat back a nearly successful Skrull invasion. The Hulk rallies the remaining heroes to make one final push against the Skrulls. In this universe, the Wasp double crosses her allies and infects the remaining heroes with a virus that wipes them all out. Banner survives once again, living to see the full conquest of Earth and the enslavement of human kind. The Hulk summons Silver Surfer and demands that he bring Galactus to devour what is now the Skrull home-world in the name of justice. The Silver Surfer sadly grants his wish, and abandons the doomed planet in disgust. Now the lone survivor of an extinct planet, Hulk finally realizes he is cursed with immortality and moves forward as the grim herald of Galactus, in search of new worlds to devour.
In Future Imperfect #2, the Hulk goes mad from a combination of radiation and grief and takes on the mantle of the Maestro in an alternate future. He rules his empire with an iron fist, driving the downtrodden denizens of his kingdom to use ancient technology so he can move forward in time.
And that's when the two Hulks face off. The Hulk is young and cocky and strong, but Maestro knows what Hulk’s going to do before he does it, and eventually manages to get behind the him, where he snaps his neck.
In The Incredible Hulks #622, Zeus gives Hulk one heck of a beat down. Bruce Banner collects an impressive posse of Incredible Hulks that includes: his son, Skaar; his estranged wife Betsy Ross; his cousin, She-Hulk; and his long-time sidekick, Rick Jones, aka A-Bomb. Banner fights his way past a who’s who of the Greek pantheon until he arrives at his destination and pleads his case to Zeus himself.
After openly admitting that he owes the Hulk and his team a favor, Zeus still tells Banner to go kick rocks. The Hulk doesn't like this and ends up mouthing off. That triggers a fight - one that Zeus wins in brutal fashion.