Find it hard to choose between Phantasm, Red Hood, and Return of the Joker. Return of the Joker is edging toward my favorite. It's at first a very competent story of an accomplished Terry McGuiness as Batman but it ends up showing pretty much my favorite portrayal of the relationship between Joker and Batman. When I think of how their rivalry ends, this is what I think of.
Conversely, Red Hood was a very interesting look at just how wickedly eternal their rivalry is, with Joker enjoying it too much to kill Batman and Batman too moral to kill Joker. We see how Batman's stolid determination not to fall into that abyss affects another character hugely and he is confronted with his greatest failure. We also get a nice look at Batman's relationship with Nightwing when they are on good terms, since the New Adventures showed Nightwing in his cranky stage. The portrayal of Joker here is really fun and divergent, landing somewhere between an overly-dark nolanesque version and the more fun, cartoony Hamill version. John DiMaggio nails it and makes a very intimidating and unpredictable killer.
Finally, Mask of the Phantasm is pretty much a classic. I consider Andrea Beaumont to be the one true love interest of Batman. No other floozy could actually rival Batman's depth and tortured soul. Meanwhile, this is perhaps the most threatening version of the Joker ever crafted, and displays the pure brilliance of Hamill as the fiendish prankster better than anywhere else. Here he is less a man and more a force of nature, warping and corrupting everything around him. This is the best set-up for the Joker that all three films do rather well - As opposed to focusing on how Batman and Joker act together, Batman's development is focused on personal drama with another character - Tim Drake, Jason Todd, and Andrea Beaumont respectively - and we see how Joker's destructive effect on that relationship. Joker shines much better in this way than by directly challenging Batman's psyche.
That, honestly, is why I prefer any of these versions to the Dark Knight's Joker. When the Joker challenges Batman directly, it's too heavy handed. In these films, he is never direct - He warps Batman's mind just with his presence. The TDK version has Joker too hung up on proving his point to everyone, but forcing morbid questions on people should be a by-product of the Joker's chaotic self, not his explicit goal.
Wow, I wrote a lot. Uhmm...
TL;DR One of those three films I guess. I can't choose. Quite possibly Return of the Joker however.