Do we count the radio edits, who are the completely the same, just some parts edited out to make it shorter? I think we shouldn't.

I'm sure there's more, but from the top of my head:

When We Were Beautiful (live Jon's vocals)
(You Want To) Make A Memory (live Jon's vocals at the start)
Real Life (higher key than the version from the boxset)
Misunderstood (the chorus sounds different, plus longer intro)
Everyday (the mix is slightly different)
Who Says You Can't Go Home (it's alrights in are sung with a 'choir')
It's My Life and Say It Itsn't So (both have breaks in the middle, but other than that are the same I think)
Blood On Blood (obviously, cause it's live)