It's hard for me to name any other series with a better ending than this. Yu Yu Hakusho comes close perhaps, but as complete as that series ended, it was not nearly as complete as this one. Every single character got his/her part of the story filled in by the end of it, and it was an overall happy ending for them all with a hint that the road isn't over, leaving us readers free to imagine how things would proceed afterwards. It was a great story and I'm happy with the way it ended.
Spoiler for Some things others might not want to be spoiled with yet.:
I really enjoyed Father's ending moments. He was so desperate for the ultimate truth, the complete knowledge of all the world and its secrets, but so focused was he by his ambitions that he failed to grasp the truth beneath the truth. That was a spectacular theme Arakawa introduced to us sicne the very beginning of the series, and was quite possibly foreshadowing what was yet to be. Ed succeeded in seeing the truth beneath the truth. He succeeded where Homunculus of the Flask had failed. The real truth was not hidden behind a set of great, gigantic double doors. The truth behind that was the very things around him, the people who were there to truly care for him, not what was hiding behind the door.
Which brings me to my next point. Ed's answer the the Guardian of the Truth made me skip a beat and shed a tear. Ed renouncing alchemy was the ultimate act to understanding that alchemy could not possibly provide all the answers, regardless of how much you learned. The real answers lay in the people around him, the world that's out there, not what was within yourself. It symbolizes just how much can be gained from acknowledging life around you rather than being self-centered and focusing on the world inside of you. That was the mistake Homunculus had made, a mistake Ed recognized he had made.
All in all, it was truly a brilliant end. Now, time to re-run it