Well, depends on the version of the mythos. Certainly it's a key event in Superman '78, which remains THE touchstone iteration of the Superman narrative in the minds of the general public (and deservedly so). It's indeed employed to good effect in Smallville, and Geoff Johns put Jonathan's death to devastating use in his excellent "Brainiac" comics arc. (Other, lesser talents have also offed the poor old fellow.)
But there are also prominent and successful versions of the story where Jonathan is still alive, even far into Clark's adulthood, like in John Byrne's post-Crisis comics reboot, or Lois & Clark: The New Adventures of Superman. I personally prefer my Jonathans alive, but can't argue that his death isn't often effective, narratively and emotionally.
They are alive in the comics again as well.