This is going to be a tough one, so I'll be going through the ones I've seen.
Memento: I think this is one of the better examples in films of tone and themes through visuals and the ending exemplifies that. A brilliant ending monologue that despite the optimistic/determined nature of Lenny, shows the bleakness and futility of his motivations.
Batman Begins: "I never said thank you."
"And you'll never have to."
Nolan could've just ended it there, with no need for two other installments and I would've been satisfied. The conversation between Gordon and Batman once again shows determination against futility and yet they shove that ordeal aside without so much as a word. Gordon simply gives him the card and they do their thing. A definitive ending to a definitive superhero movie.
The Prestige: I must admit, on my first viewing the ending didn't quite have much impact on its own merits, mainly because as soon as it was over I watched the whole film again. But of course, on the second viewing the dialogue really seeped in, as we see the true motivations and acts of the characters, leaving it up to us to see who was right.
The Dark Knight: This ending left a massive impact, punctuated perfectly by the score, writing and cinematography. When viewed on its own, it gives a feeling of sacrifice but going through with it all. Of course, it was more of a fall than realised at first, which makes it kind of more harrowing looking back. Still, it did its job well and that's what matters.
Inception: My favourite of the bunch, Inception just wouldn't be complete without its ending. Every time I see the film, I get a different interpretation of it all that culminates itself every time with the ending. With one of the most beautiful pieces of music I've ever heard, it sticks with me to this day and most likely will for the rest of my life.
The Dark Knight Rises: Thematically, The Dark Knight Rises is the odd one out of Nolan's films. All his films have dealt with lies, to deal with grief or for the greater good. This film is the first time that the true consequences have been shown in full. Bringing futility to the forefront. Yet also determination, more so than ever before. And it all pays off. Some might call the ending bittersweet but once those classic drums return for the last time, it becomes one of the most heartwarming and inspiring endings ever put on screen.
So yeah, this is a tough one. But in the end I'm going to have to go for The Dark Knight Rises. Maybe it's just the impact of it only being out last month. However, while it might not be my favourite film, it gives a complete sense of closure like no other of his films.