I saw them live on that tour, and Alone Together will have a special place in my heart forever because standing in a crowd of several thousand people singing it is essentially a religious experience.
It's a cast recording rather than an album album, but Hamilton has to be my favorite. Fall Out Boy's Save Rock and Roll and Dave Carter & Tracy Grammer's Drum Hat Buddha are some of my other favorites.
Also thank you for reminding me that Breaking Benjamin exists and that I love them!