Batman: Hush

I'd have to say that this is one of the better Batman animated films I've seen - and I've seen most.

The story seemed more "adult" (without trying too hard and being too much so), with a more serious tone, but it also had a good balance of darkness and humour. I haven't read the comic or graphic novel so I can't compare it to that, but on it's own I'd have to say that it was well done. The characters were fleshed out enough for me, and the ending wasn't the predictable one I thought it was going to be.

Off the top of my head, the only one I can think of that tops it is Under the Red Hood.