It's got to be "Brand New Start" for me. Everything about this song knocked me over, both when I heard the live acoustic performances and again once the album version surfaced. Myles has never sounded smoother than in the verses, and the choruses come along and blow every other modern vocalist out of the water. Mark has the slickest fills in the choruses, and his solo is among his most emotive ever. The drums are perfect, and to this day I love the simple beauty of the dual cymbal crashes between measures. The bass is slick and elegant.
I considered "In the Deep" as a top contender, and even though I love it, such a new song can't surpass the timeless love I've had for BNS, what, twelve years later.
Bleed and OYE would compete for #3: the former with its powerhouse drums and tear-jerking guitar solo, and the latter with is timeless singalong bridge.
I agree with Greg, I've never gotten the hype around Ghosts. It's a good song, and I love the way its dark bridge interrupts its otherwise summer nostalgia feel, but it just doesn't stick out as top tier to me.
TOS is last for me. I like the riffery and lyrics, but the melody just doesn't compete.