I was always a fan of Batman: TAS. I've only watched other parts of the DCUA and not really much of the later Batman stuff, so I can't comment on those. But I do agree with what Turtletrekker
said in the opening post, that Mark Hamill was really the fit for the Joker. Like Batman himself, Joker requires a bit of balance to keep him from being either too openly violent or too silly, and I think TAS did that wonderfully. It also gave us Harley, so it was 20% more awesome.
I recall reading an interview which I think was Paul Dini (not Bruce Timm, though I could be wrong). He mentioned the worry that some people would be offended by a scene in "The Man Who Killed Batman" where Harley plays Amazing Grace on a kazoo
, but it seems that didn't happen. He did say he was glad her voice actress, Arlene Sorkin, managed to do it in one take because the cast broke up laughing immediately afterward.
Bruce did say that he and Paul came up with the story in a discussion about making an episode where Batman didn't actually appear or did very little.