I'm surprised no one's mentioned Luminous Times yet! That's a big one for me.
To that I'll add Love Is Blindness, Stay, Always Forever Now, In a Little While, and, a tad embarrassingly, Crumbs From Your Table (my mom used to play that a lot in the car's CD player growing up, so I have fond memories of that one).
EDIT: I'll throw Invisible in there too. I only started liking that song a couple years ago, so it has a freshness that a lot of U2's better songs lack for me, and I was reunited with it at a time I needed to be.
EDIT 2: Like a Song... deserves the honor most certainly. Another thread reminded me of it. I was too focused on U2's more romantic emotionalism.