I saw the final three shows on this tour, and it was an incredible experience. Between the shows I saw, only three songs were played thrice.
In hindsight, maybe the Boston show was the best. Incredible versions of songs not on Score... Take the Time, Wait for Sleep, Learning to Live, Strange Deja Vu, Endless Sacrifice, A Fortune In Lies.... just an unreal setlist, and they were on fire in 2006 performance-wise.
But RCMH was my favorite show I've ever been to. I personally LOVED the setlist. As a newer fan at the time, it was my first time seeing a lot of that setlist. And many songs, they have not performed again: Another Won, Innocence Faded, Raise the Knife, Six Degrees of Inner Turbulence (in full), and the rest of Act 2.
As many have said already, this was a special moment for the band, and they were at the very top of their game and career. It's never been the same since, though I've enjoyed everything they've done after.