You know as ridiculous as it is, overplayed and popular and all, I still think they never topped In the End. Something about that song is tremendous. Reminds me of my college exam days (in a good way). Hybrid Theory is without a doubt their best album. They got progressively worse after that. When you are lost, tired, and worn out mentally, In the End is a great song to sing out loud.
By the way, a close second is Numb. Fantastic single on a rather dull album.