Gordon is pretty active in the Animated Series.

My favorite has to be Mask of the Phantasm, because it's set in the cartoon universe. This choice, however, is not out of nostalgia; I hadn't seen this one until about 3 or 4 years ago. I think it truly nailed Batman, even if it had a bit of a hokey origin story. The plot shows that the authorities aren't always buddy-buddy with the police; in contrast, in The Dark Knight, it was that way because Batsy wanted it. Also, I know it's cliche, but Kevin Conroy as far as I'm concerned truly has the Bats voice down: commanding and awe-inspiring. Much better than the grunts of Bale.

If I had to pick live-action, I don't think I could. I think the Burton movies really had a better feel for how dark and slimy Gotham is supposed to be than the Nolanverse, and I really love the Batcave's design, but I can't deny the great things in Begins/Dark Knight either.