I don't know... This list is kind of all over the place for me. First off, their logic is flawed. The number 96 is so random. Their statement about the renaming of the series in *season 3* doesn't make sense. There are 85 episodes of Batman TAS (65 initially from 1992-1993 plus 20 added later in 94/95). Then in 1997 it returned under the name The Adventures of Batman & Robin with 24 more episodes for a total of 109 (These also aired as part of the Batman/Superman hour). So most fans either use the number 85 for just Batman TAS, or 109 as an all inclusive number...96 isn't a *thing*....
Anyway, my personal favorite #1 is Jokers Favor. Having it mid range on this list is incomprehensible. I remember recording the episodes as they first aired. Cat & Claw Conspiracy part 1 aired on Saturday Morning. On Leather Wings was a special Sunday night premiere, and all week long I recorded the episodes. They aired the Clay-Face 2 parter, and a couple others, then on Friday, Finally we got our first Joker episode!
My friends and I knew from attending SDCC just a couple months prior, that Mark Hamill was going to do the voice, but of course we were skeptical. All that ended, as soon as we started listening. This is just an amazing, and funny episode in so many ways. Most tout its significance of being the first appearance of Harley Quinn....but it's not even that, The Joker is just so great in this episode, and also how a regular shmoe can rise up after being bullied so long and turn the tables.