Perchance to dream is my favorite episode. It just happens to be kevin conroys favorite episode as well.

Mine is Two-Face Parts 1 @ 2 because of his former friendship with Bruce Wayne. I also liked the interpretation of Harvey Dent's repressed dark side because it was psychologically disturbing. Also his coin is the item that Two-Face needs to maintain his double personalities. And without it or when it is on edge, Two-Face is helpless, cant make decisions and doesnt feel "complete". In other words, Two-Face is completely dependent on the coin, because this item serves as a motivation for his actions.
Still i felt he didn't get enough screen time and they never use Two-Face to rob stuff during the day to give to charity because Two-face is suppose to be the lesser of two evils. I mean Batman said he fears Two-Face more then any of his foes and it's something the writers don't seem to acknowledge threw out the years. And he disappears with no mention of his whereabouts in Batman Beyond.

It's mine too. It has my favorite portrayal of Mr. Freeze, and it mixes great story telling with some of the greatest fights and visuals in the entire series.

That was a great one, but "Heart of Ice" gets my vote. I was a Mr. Freeze fan before, but what the writers did for his backstory in that episode was legendary.