Lightning Lord electrocutes Lana into a charred remain.
Myxzptlk gets torn in half in the finale. Despite him being a nebulous 5-d being at the time, it's still rather unnerving to see his image splitting down the middle.
Sure, the bad guy deserved it, but seeing Krypto tearing out Kryptonite Man's throat is really brutal. Not helped by the fact that Krypto dies of Kryptonite radiation.
In real life, Julius Schwartz was discussing the story with Alan Moore, and told Moore that he wasn't sure who would write it. Moore alledgedly responded by standing up, grabbing Schwartz by the throat, and threatening to kill him if he wasn't the one who wrote the story. There's a reason Alan Moore is considered a Memetic Badass among comic writers - he can be terrifying.