That prayer from 1000 Hurts got me laughing the first time I heard it. I also didn't know who it was or where the song was going to go, which made it so much funnier.
Another couple I forgot to mention: three spots on the new Milemarker album.
-The opening of the song "Virtual Sex," for starting with a quiet solo bass riff and the line "All this virtual sex."
-Later in the same song, the band goes quiet and you hear a cell phone ringing; the first time through, it sounded like the singer then yelled "man, who's that calling in the MIDDLE OF THE SONG?!" (it was actually "middle of the night"
-The song "Landlord," wherein I first thought the singer randomly screamed "IT'S 1996 YOU MOTHERFUCKER!!!!!!"
But isn't everything funny when you hear it wrong?