Off the top of my head, SpongeBob SquarePants, Danny Phantom, Fairly Oddparents, The Big Bang Theory and It's Always Sunny in Philadelphia all have jokes, if not the main plot point of the episode, that are just mocking the existence of LGBTQ people.
Looks like this happened after season 3, so it all checks out. Just more evidence that Hillenburg was right in wanting to end the series after the first film released.