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.
I find Lindsay Ellis a little questionable these days, but her new video on Pop-Culture Transphobia is illuminating. I never realized how omnipresent the vomiting-at-trans-people ""gag"" was