I prefer the acoustic version of Prayer. The electric version can be a lot of fun live, but I never sit down and listen to it at home. The only one I quite enjoy listening to is the one from Wembley '95.
I agree with you on Superman, don't really like the album version but liked the acoustic version. Blood On Blood can be great acoustically (The one they played at Virgin Megastore in the 90's is amazing.). In These Arms/I'd die for you were great at the These Days tour. Hmmmmm....other than that: maybe Born To Be My Baby.

And Santa Fe in Barcelona was touching, I don't know if I prefer it to the electric version, though. Probably not.