Well in Batman Beyond Return of the Joker, it was explained that Joker continued to live on after his body died by planting a microchip on Tim Drake that carried over his Gene sequences and I guess his memory somehow as well.
I remember in the crappy edited version of that awesome movie, they added a line about how he got Jarvis Tetch aka the Mad Hatter to design the microchip system for the Joker. I think Joker could have used this multiple times, hence when he appeared to be eaten by a shark in the Laughing Fish episode, when he died in Superman/Batman, and when he fell to his death in "The Killing Joke", he might have really died all those times and just had another host body lined up.
"Nobody knows anybody, not that well..." - Miller's Crossing
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