Alas, Poor Scrappy: Jason wasn't exactly the most favored character at this time, but lots of fans thought his Family-Unfriendly Death was... a bit too much. Frank Millerof all people said, "An actual toll-free number where fans call in to put the axe to a little boy's head... to me the whole killing of Robin was probably the ugliest thing I've seen in comics, and the most cynical." A major factor to this is most likely Wizard Magazine, which had a horrible habit of slamming characters or concepts they didn't like. There was even an April Fools Top Ten of Characters that should Stay Dead and Jason was #1. Thus, if it wasn't how brutal Jason was cut down, it was certainly because certain people wouldn't stop making fun of it. Which was arguably the point - fans wanting to see Todd written out of the series got preciselywhat they wanted, courtesy of...
Complete Monster: The Joker is as monstrous as ever. After escaping Arkham Asylum, during which he kills a number of people, the Joker steals a nuclear weapon with plans to sell it to terrorists during the Lebanon civil war. He also blackmails Jason Todd's mother Sheila into helping him obtain medical supplies that he withholds from the starving to sell them on the black market, replacing them with laughing gas that, when set off, will kill thousands of people. Capturing Jason Todd, the Joker beats him with a crowbar before killing him and Sheila with a time bomb. After getting a position as the Iran representative, the Joker holds a speech at an assembly, only to try and kill everyone in the building with poisonous gas.
It's suspected that Lady Shiva could be Jason's mother. While drugged with truth serum, she states that she's never had a child. Years later, her daughter, Cassandra Cain, becomes the second Batgirl. And Bruce notes that she seems to be about Jason's age. Epileptic Trees have led to some fans theorizing they're siblings because of this.
Batman mentions how the American embassy in Iran was taken over. The current actor playing Batman, Ben Affleck, made a movie, Argo, on the events of that.
In a dark mix of this and Harsher in Hindsight, Superman is called in by the government to stop Batman from killing the Joker as revenge for murdering his son. There's a dark, ironic chuckle to be had at this in light of Injustice: Gods Among Us, where their roles were reversed.
It Was His Sled: Jason's death, and Tim Drake taking the mantle of Robin in his place.
Misblamed: In-universe. Whenever the story is referenced later, Jason's mother, and the role she played, are completely forgotten, leading to writers blaming Jason for his own death.
Again, The Joker, as he brutally tortures Jason Todd (the second Robin) right in front of his estranged mother Sheila, before killing both in an explosion.
Hell, Sheila herself for tricking Jason into the warehouse so that Joker and his men could ambush him when his guard was down. Sheila's reaction to this? Grimacing, then lighting a cigarette.
Narm: Jason's death is the thing everyone remembers about this story, but few remember just how bizarre it gets afterwards. In the last issue the Joker becomes the Iranian ambassador to the United Nations, and gives a speech that basically says that the Iranian government is just like him, because they both hate America. This was likely an attempt at being topical (the Iranian Hostage Crisis was still fresh in people's minds), but it makes very little sense and is impossible to take seriously.
What an Idiot!: What, exactly, do the United Nations expect a homicidal maniac like the Joker to do when he addresses them? Why on Earth did any of the other delegates even show up for his speech?