Wow, what an intresting topic. You should make one for Meteora and MtM too. Anyway, I'll just post one for me.
Least Signature Guitar Riff:
In The End
It feels like Brad made up this part within five minutes, I mean honetstly, he could've at least make up some intresting strumming patterns for the chrorus, and a more complex harmonic riff in the verse, like one in With You or PMA.