Acoustic-specific songs, no. I've always felt that it's a lot easier to strip a song down to an acoustic format and make it sound good than it is to take an acoustic song and make it rock. There isn't a lot you can do with an acoustic song other than play it straightforward the way it was recorded. I wouldn't mind them doing more songs that incorporate acoustic guitar like TLTGYA did, though.
That being said, I really want them to do an MTV Unplugged set at some point. Especially after the release of MTM, they now have a pretty large number of songs that would work in an acoustic format.
As for what I think they should do to their songs live, I really wish they would bring back the Reanimation bridge to One Step Closer. Combine that with the extended intro/outro and it'd make the ultimate live version of that song. I think they should move Rob's drum solo from Bleed it Out to another song, although I'm not sure which one would work. They should also do some more experimenting with making songs blend into each other like they did with Figure.09/From the Inside and Breaking the Habit/Numb on PR04. They had a nice one going with the piano transition from Numb to Pushing Me Away in the early part of 07, but Mike started slowing it down over time and it never worked quite as well after that. One Step Closer into From the Inside at Milton Keynes was cool, they should do that one again.