"Underrated" could mean different things. Underrated by us U2 fans? The general public? By the band? I might have different responses for each group, but overall I'd say:
1. Native Son. Obviously with hindsight we can see how iconic and important Vertigo was, but I'll forever believe that they should have gone with Native Son instead. It's just the better song. It struck the perfect balance where you could find a political message in it if you wanted to (and with the second year of the War in Iraq, the upcoming '04 election, etc), but also vague enough that you could just enjoy it as a rock song no matter your political persuasion, which is where the disaster of American Obituary falls short. A ballsy choice, certainly, but I think it would have been a big hit.
2. Love You Like Mad. One of my favorite non-album songs. I have it replacing AMAAW on Bomb, and I like AMAAW a lot.
3. A Sort Of Homecoming. I've got it as their 7th greatest song, but nobody outside U2 world knows it. Incredible that a group of early-20-somethings wrote this. They certainly had good, even great songs before this, but I think this is their first song with truly remarkable lyrics.
4. If You Wear That Velvet Dress- a top 25 song for them, often overlooked on Pop.