By far my favorite of his work is The Civil War. I find that one to be especially powerful and moving. Sure, no doubt it's because of the topic, but it is also due to segments ("A New Birth of Freedom") such as the one at the end of the fifth episode, "The Universe of Battle."
Now unfortunately (and ironically, since it's from PBS) the most stirring moment of this for me (and an example of Ken Burns' potently effective style), is cut from the video above. It comes during the last few seconds, just before the final credits of the episode begin. As Waterston finishes reading those sacred words, and the final chord of "Ashokan Farewell" fades away, there is silence, the camera lingers for three or four seconds on that great portrait of Lincoln (taken by Mathew Brady, I believe), and the screen fades to black. I blubber like a baby almost every time (dammit!), for the man, looking thoroughly spent and depleted, his sacrifice, and due to the beauty of the filmmaker's accomplishment. Please experience that at around 1:30:43, at the end of this complete version of the episode. It's subtle, but nuance is what life is so often about!