This is exceedingly common in American superhero comic books, to the point that whenever a popular character dies, it's a given that they'll be back on within no more than five years. At one time, it was said that "Nobody ever stays dead in comics, except Bucky, Uncle Ben, and Jason Todd." Naturally, since that phrase was coined, Bucky and Jason Todd have since been recalled to life.The Marvel Wiki site has 115 characters currently tagged in the category of "People who used to be dead but aren't anymore".
Why is this? My personal interpretation is that the main problem is that comics companies are really nothing but intellectual property (copyrights and trademarked character designs and such), and to the extent that corporate directors are required to work "with a view to the best interests of the corporation", then the executives of those companies are in some sense required to milk every character property for every cent it can produce. If company X owns the rights to deceased character Y, and there are any customers who would purchase a book if character Y were brought back in it, then it can be argued that the company directors are legally required to bring back that character and produce that book. (That's a bit of a legal stretch, but it highlights the real principle: if Y can make money, then Y comes back from the dead.)
So of all the dastardly acts of vengeance, and cunning deathtraps, and cosmic-beating sacrifices one can imagine, it seems like no villain in the universe has any chance of permanently putting down any hero or antihero character... right?
Well, here's one way you can do it: Lose the license to the character.
If company X entirely loses the right to publish character Y, then they really-honestly won't be showing up anymore (at least in that company's universal continuity). One common way for this to happen is via cross-market toy promotions, where the rights are held primarily by some outside toy company, and the comics publisher has a limited term to write stories for it: instances of this at Marvel would include Shogun Warriors, Transformers, G.I. Joe, and perhaps most notably, Rom. Rom was intimately tied into the rest of the Marvel Universe in many ways; I know that the Fantastic Four appeared in Shogun Warriors, and Spider-Man at least once in Transformers. Nonetheless, these characters won't appear again in Marvel continuity because they no longer hold a right to publish them; in fact, in many cases Marvel can't even republish the stories in the now-standard trade-paperback formats, such that they become relatively rare collector's items. The same could be said for Godzilla which was also smack in the middle of the Marvel world when it was being published, fighting against S.H.I.E.L.D. and such from the first issue. (I don't think you'll find an entry for Godzilla in the Official Handbook of the Marvel Universe, but you will find him referenced second-hand in places like the entry for Red Ronin: see here, volume 3, p. 207-208).
Now, it's not like any of the characters mentioned above are actually dead; they're just gone. Usually the writers of those books, upon being cancelled, write some fairly upbeat wrapping-up story with the characters victorious and basking in a sunset of glory. (Interesting example: Rom is so deeply woven into the fabric of the Marvel cosmos that he keeps being referenced as a past epic hero, or even appearing in-book in his human guise, it's just that no one can refer to him by his name "Rom" anymore. Neither, again, can his old stories be reprinted. See near the end of this article.)
But it does bring up an interesting prospect, in that if you're a writer on one of those licensed comics when it gets cancelled, you might consider actually killing one or more characters off in a dramatic, climactic end-story. If you do that, then you'll be able to stand in the almost uniquely rarefied club of people who who killed a comic character in a way that they really can't come back.
(For supporting fodder on this plan, consider the article in the final issue of Game Developer magazine this past year, "In the End, Tell the Truth" by Jason VandenBerghe, which makes this compelling argument: "As a game designer, you are more free when crafting your ending than you are for any other piece of your game." Download it here.)