Hands Held High, Iridescent, The Catalyst, The Messenger, and possibly Wretches and Kings. Basically, any song with any kind of gang vocal. There are are some songs that he just sings live because there are many vocal parts, like TLTGYA. However, on the album version, it's just Mike and Chester layered together.
If he's on the "hey hey" part of Wretches and Kings, you can probably add When They Come For Me to the list too, because I think the "hey hey" part at the end of that song is a re-sampled vocal part from W&K that's been slowed down slightly.
Yeah I've got the Road to Rev DVD and I think his singing is awesome in TLTGYA. He should be more self-confident, though.
He and some of the other band members do backing vox on a bunch of songs now during the live shows; obviously, there's the "A Thousand Suns" material, but Phoenix sings with Shinoda on the outro for "What I've Done" as well
When I went to the Webster Hall show in theaters in 2007, when they showed the alternate DVD of making of MTM, Mike showed how the chorus in HHH is actually all the band members singing HHH at once, and he made it so you can only hear one of the vocalists and it was Phoenix. That was amazing.