Except that with Batman and Superman, they don't ignore everything that happened. Especially in the case of Superman, they talk about that stuff all the time, and the Doomsday character is always coming back in different incarnations, most recently in last month's issue of Superman. Before that there was a Kryptonite-laced mutated Doomsday soldier created by the US Government called "The All-American Boy" in the Kryptonite arc of Superman/Batman. Characters reference Superman's death all the time; Batman had a great, bitter line in Infinite Crisis a few years ago about how the last time Superman inspired anyone was when he was "dead."
Yeah comic book deaths are never permanent, blah blah blah, but don't act like these stories never have any lasting impact. There are tons of things that came out of the death and subsequent resurrection of Superman that still reverberate today.
Likewise with the Knightfall storyline. I mean come on: Bane. An excellent addition to the rogue's gallery. Elements of the character were even utilized in the buildup to RIP: one of the three "Replacement Batmen" was a dude pumped full of Bane's venom; a hulkish monster-Batman. Don't forget that Jean Paul Valley's Azrael: Agent of the Bat series ran for eight years and only ended five years ago.