The Requiem, to A Thousand Suns as a whole. For a single song? Does Tinfoil to Powerless count? If not; The Catalyst. Those opening notes set the tone for the whole song. It's so minimalistic compared to the rest of LP's stuff, and that's what makes it my favourite.
Faint I always loved the electric strings at the beginning. When I was growing up it was an eargasm to hear that.
Somewhere I Belong. As shitty as the actual song is when it comes to the lyrics, I really do like the reverse instrumentation in the beginning.
"No More Sorrow", hands down. "When They Come for Me" is awesome too (it's also my favorite song off A Thousand Suns).
If you count Tinfoil as an intro to Powerless (I know it's really a transition song), I'd say that. If not, I'd say No Roads Left. Love just hearing the pure guitar in the beginning.
God, there's so many... BITS, Catalyst, WTCFM, Papercut, LITE, What I've Done, PoA... And of course Forgotten
In the End is one of my favourites. Whenever that song starts, I feel good. I also love the intro of Lost in the Echo, it makes me feel so energetic! When They Come for Me is pure awesomeness as well, I really enjoy those drums. And No More Sorrow is great too, it makes me want to rock out to it. The intro of The Catalyst gives me goosebumps. I remember hearing it for the first time, it was mind-blowing.
Fallout, the intro song to The Catalyst, gave me goosebumps when listening to it. One Step Closer intro is pretty badass as well.