A Change Of Seasons or In The Name Of God. Really all of those are among their best, except A Mind Beside Itself (well it's good, but no song really stands out as amazing for me and it's not that great as a whole, just three decent but different songs).
ACOS / INTOG
Octavarium / ITPOE / TCOT
Six Degrees
ANTR
A Mind Beside Itself
For me anyway. Only a few great songs are anywhere near the best (top 5 in my list) of their "long songs" (Metropolis, The Glass Prison, This Dying Soul, Learning To Live, Blind Faith, Endless Sacrifice, Take The Time, Home, etc.)