Family-Unfriendly Aesop: Women, if you think you've been sexually harassed, don't tell anyone, because you're probably wrong and will ruin an innocent man's life if you make a big deal out of it.
Harsher in Hindsight: Homer's whole plight becomes more uncomfortable when, in 2014, an article in Rolling Stone discussed the story of a rape at the University of Virginia, bringing strong support for the victim, including fines and suspensions, until other investigative journalists discovered that the entire story was a hoax. Unlike this episode, the reporter was blasted for not even attempting to corroborate the story.
Inferred Holocaust: While escaping the candy convention at the beginning, Homer mixes poprocks and cola and turns it into a grenade, causing a massive explosion and presumably killing hundreds. This is never mentioned once afterwards.
It isn't uncommon for more important stories to be overshadowed by exaggerated scandals like Homer's alleged sexual assaulting.
Memetic Molester: Homer drooling lustfully at the Venus gummy candy on Ashley's crotch area, before making a grab for it ... even though that is exactly what Homer is clearly wanting (the candy), not to satisfy a sexual desire.
Misaimed Fandom: Many people seem to believe that this episode exists to make fun of feminists and people who accuse others of sexual assault.
Some Anvils Need to Be Dropped: Editing news for entertainment purposes, as well as over-the-top or wrongful accusations, can destroy peoples' lives, and you shouldn't believe everything you hear on TV.
The media needs to watch its distance during allegations or it will take advantage of the situation and actively harm both parties.
Just because the accused is found "Not guilty" doesn't necessarily mean that the justice system is flawed, thus deserving to get scrapped. Due process is exactly that, a process.
People who deliberately lie about rape or sexual assault are no less harmful than real perpetrators, because they make real victims more worried about coming forward for help since they're already concerned that nobody would believe them. He points out how even though the 2014 University of Virginia rape story from Rolling Stone Magazine was revealed to be a hoax, people were still supporting the person who lied about the whole thing, comparing it with a Phony Veteran still being honored as a war hero even though they're proven not to be one.
Values Resonance: Much like the movie Network, this story is still considered a spot-on satire against how scandals (particularly sexual ones) are sensationalized by the media in this day and age, despite being a cartoon from 1994 (and, had the writers used the original idea of Homer and Lisa arguing over "the double standard" between men and women, it still would have been relevant, as it's one of those things about modern society that hasn't been resolved over time). The writers acknowledged this in the DVD commentary, even arguing that things have gotten worse since this episode originally aired.
The Woobie: Homer is undeservedly put through hell by the producers of Rock Bottom and the ensuing mass media storm.