In one scene, Lisa asks Milhouse to send Nelson a love note from her, but Nelson is led to think the note's from Milhouse himself. Cut to Milhouse being led away in a stretcher to an ambulance (with the paramedics telling Lisa that Milhouse can't hear her — not because he's dead, but because his ears are packed with gauze). It really stops being funny after the highly publicized rash of suicides and murders from bullying, especially anti-gay bullying. The setup of the scene is horrifyingly very similar to the murder of Lawrence King in 2008. Even the writers back then (according to the DVD commentary) had to be careful not to show Milhouse as brutally beaten and thought the idea of Milhouse getting Mistaken for Gay and assaulted for it was in bad taste.
One poster in Nelson's room has the caption "Bomb the Arabs and take their oil," which is pretty much what the War in Iraq in 2003 was accused of being about.
Values Dissonance: Jimbo says "That is so gay!" when commenting on Nelson kissing Lisa. Back in the 1990s, it didn't raise any problems. Contrast that with the 2008 "Treehouse of Horror" story that had a giant pumpkin attacking the schoolkids during a Halloween dance, Nelson's line "The Grand Pumpkin is super gay!" was met with backlash from anti-gay defamation groups who set out to stop people from using the word "gay" as an insult for something considered "weak" or "stupid".
What An Idiot: A lot of the actions in the subplot of Homer using an autodialer is teeming with stupid decisions and actions, including:
The autodialer being tossed in the trash following Jimmy the Scumbag's arrest. If Wiggum took the autodialer with him in the first place (as he does need it as evidence of Jimmy the Scumbag's crime), then none of this would have happened.
No one in Springfield (not even his father, Abe, and his neighbor, Ned Flanders) thinking to rat Homer out to the authorities since they know him and are familiar with his voice.
Homer trying to blame Marge for having the autodialer, despite that he gave his name, address, and phone number in his message.
Chief Wiggum telling Homer to bring the evidence with him to court rather than Wiggum taking the bullet-riddled autodialer himself (and Homer actually bringing the evidence against him to court, just so he can tape another scam message). Wiggum was even stupid enough to tell Homer that there'd be no case if Homer didn't comply.
In the A-story, there's Nelson's "Hey, Willie, catch the football" prank. You'd expect Groundskeeper Willie to demand that Nelson put down the beehive. Instead, Willie goes long and gets stung severely when he does catch it.
In fairness, he might not have realized it wasn't a "football" until it was too late.