I can't say, I have to many favorites....but I will say that at the current moment I like Breaking The Habit.
It has to be The Catalyst. It sums up the overall sound of A Thousand Suns (my favorite album from them) and it was the first song I saw them performing live back in 2017.
I think Waiting for the End is their best work, that song means a great deal to me. Leave Out All the Rest is a close 2nd. I could list countless more that I love while I'm at it, but it's those two that are especially important to me.
In The End is my all time favourite. (It was the first LP song I heard back in 2001. It got me hooked ever since) Newer favourite is either The Catalyst, A Line In The Sand, No More Sorrow or Final Masquerade (can't decide lol)
It's either When They Come for Me or Waiting for the End for very different reasons. Both are fantastic.
Hard to pick just one, Id say my favorites are: Part of me -from childhood Pushing me away - beautiful melody Breaking the habit - DEEP