It's really hard to pick which one specific one from Into the Woods, but I'd either say "Last Midnight" or "No One is Alone".
First, the case for "Last Midnight". The song isn't really that luscious or beautiful to listen to, but in my opinion, this isn't important in theatre songs: a song from a musical is meant to further character. And, in the case of the witch, this is a really good song in furthering character. It shows her undying love for Rapunzel, as she demonstrates she'd rather be back the way she used to be rather than not see her daughter's death avenged, and it just shows the amount of control the witch really has. She terrifies the characters without any of her characters, and even though she's supposed to be the villain, she points out all of the other's selfish desires and how they're just as bad as her. She doesn't say that she's good either, but she states she's "right", demonstrating the accuracy of everything she says.
While "Children Will Listen" is much more direct in sharing the message of the show, and it does make me cry, I have to go with "No One is Alone". First of all, it is the climax of the show, and it is packed with emotion as a result of the characterzation throughout, so its timing in the show is impeccable. Secondly, the song gets its message across, the show's message, in a way that comes naturally, as it's the characters telling these two children, in a time of need, that they really can't say what is wrong or right anymore, based on everything they've seen. And, it also helps in The Baker's characterization of a father. While at first he's just as confused as Jack, screaming, "I don't know," when asked if it was right if the Steward killed Jack's Mother, he grows to show the maturity of a father by the end of the song, telling Jack all he can say, but just as Cinderella started off the song, comforting Jack, saying that while he is not alone, he also need to be careful about this, as he can't go after his own selfish desires. And, the ending in the OBC, where they are cut off by The Giantess right before they are able to finish the song only makes it even more realistic, and gives the song much more emotional depth.
I know I probably butchered the characterizations, but these two songs define what a broadway song should be. It should only serve to further the characterization of the characters, and these two songs do this excellently.