I'm a bit late to join the thread, but here's my list:
Waking Hour: Momentum, Gravity, Lullabye For a Stormy Night
Warm Strangers: Feather Moon, Harbor, Shine
Dreaming Through the Noise: Nothing Without You, Pontchartrain, Recessional
It's funny; I bought Warm Strangers on the strength of "Homecoming",... and it's not even in my top three. Similarly, I really, really like Now Three, and before the album came out, I was sure it was the most beautiful song ever; but something is missing in the recording, and the three I chose for this poll are just SO good that Now Three got bumped off my list.
Of course it's only natural, being a serious musician, that the most inventive songs, musically, would make my list. This includes Momentum, Feather Moon, Harbor, Pontchartrain, and Recessional. And I originally got hooked on Nothing Without You when it was a guitar song tuned in open-C# tuning with a lot of nifty half-barre chords. The fact that I still like it as a piano song in the key of D just means it's a good song anyway.
Lullabye and Gravity I like for much simpler reasons: because Lullabye is gorgeous and Gravity rocks! And Shine is a simple song but it has a positive message, and as much as I like the music for My Medea, words do occasionally make a song.