I think this is the forum I remembering seeing the thread on... Anyway, for those curious, the fate of Ledger's Joker after The Dark Knight is revealed in the novelization of The Dark Knight Rises. Here's the excerpt:
“Now that the Dent Act had made it all but impossible for the city’s criminals to cop an insanity plea, it (Blackgate Prison) had replaced Arkham Asylum as the preferred location for imprisoning both convicted and suspected felons. The worst of the worst were sent here, except for the Joker, who, rumor had it, was locked away as Arkham’s sole remaining inmate. Or perhaps he had escaped. Nobody was really sure. Not even Selina.”
And the source.