I've been watching Batman: The Animated Series on and off for the past few weeks, and I'm roughly 3/4 of the way through it now. (I'm just before they changed up the character designs to streamline them and make them fit with Superman: The Animated Series) I watched the show when I was a kid, but I only remembered a handful of episodes, and there are a ton of great ones that I didn't get to see. (also, I watched Mask of the Phantasm, which is absolutely phenomenal)
So far, any episode that heavily features the Joker, Harley, Two-Face, or Mister Freeze has been amazing. Ra's al Ghul's introduction was outstanding, though his later episodes didn't quite live up to that. Kevin Conroy's Batman portrayal is pretty much the definitive version of the character, though that goes without saying.
It's not perfect - it honestly feels like they didn't know what to do with the Penguin (outside of the episode Birds Of A Feather, where he tries to fit into high society and it quickly becomes clear that he has no idea what he's doing), and Catwoman doesn't get the sort of focus that I'd expect. (her episodes feel few and far between)
Still, I'm glad that I got the series on DVD and sat down to watch it. I'd be hard-pressed to pick my absolute favourite episode - Almost Got 'Im was a highlight (Batman's villains play poker and talk about times where they almost got/killed Batman), but Heart Of Ice, the Two-Face two-parter, the Demon's Quest two-parter, Beware The Gray Ghost (featuring the late, great Adam West), Perchance to Dream, Harlequinade... I could go on and on and on.
By contrast, I don't remember much about Superman: The Animated Series (just a few episodes/moments), and I didn't watch Justice League or Justice League Unlimited when I was growing up, so I'm looking forward to watching those.