Hmm, I don't know about flawless, but I am a really big sucker for endings with "plot twists" that further explains what we saw in the beginning. This is why I liked Madoka so much, [obvious spoilers] but I really liked how Homura ended up being the cause of it and I liked how it eventually led up to Madoka being able to make such a large wish. :3 I thought this was especially intriguing because in the first episode we thought things were semi-normal, however it's explained later that it's all Homura's doing instead.
Okay, also again not flawless, but I really liked Clannad After Story's ending a lot, and how Okazaki was able to go back and live a happy life after living through such a sucky one earlier. I kind of saw it coming, but the way they did it was nice, and it gave reason to why we spent the entire first season (which I didn't actually like very much) focusing on other girls instead of Nagisa/Okazaki.