There are a couple moments that come immediately to mind: the first is, obviously, the oft-reprinted few couple of panels from that Denny O'Neil story where Superman EATS Kryptonite.
Some of the less-famous shocking moments have to be during the Cary Bates story where the space-Amazon Quazars attack earth, and in order to grant immunity from the Quazars' mind control, Superman has to KISS Lucy Lane. And not just a chaste peck - a big, fat, horny smackeroo using the tongue. Boy, I'm sure Lucy hated every second of that.
Jimmy Olsen's Superman's Pal, but there are definitely limits.
Another would have to be that Cary Bates story with the woman that claims Superman crippled him. In it, Superman takes a missile directly to the face, and LAUGHS. Big Blue then sticks his thumb out, points it at his chest-symbol and says,
"Do you see THIS? Do you know what this STANDS FOR? It means I can mop up the sea with saltwater scum like you...and you can't do a THING to STOP me!"Wow, I sure wasn't expecting that.
Another shocking moment would be in that Jerry Siegel/Curt Swan 1960s story where a cabal of villains captures Superman and puts him on trial. Superman literally PLEADS for mercy in the most pathetic way possible, trying to bribe all the villains in exchange for saving his life. He offers Saturn Queen eternal youth, turning Lightning Lord's lightning power to nuclear power, Lex Luthor a group of Kryptonian super-weapons that are buried on earth (which is especially selfish of Superman, considering all the mayhem Lex would consequently release with them on innocent people).