There were multiple episodes that I remember watching as a child (In fact, I think I have seen all the episodes except the recent ones in the last 3-4 years). The one where they make a movie due to the new "James Hound" movie is rated PG-13, the Christmas movie about uncle frank, the Mr Rogers episode where he comes and stay in Arthur house(there was another episode like this except Arthur's teacher Mr.Ratburn) and so much others. However, one thing that was stuck in my head ever since I saw it was an episode where Muffy was watching a Backstreet Boys music video and Francine calls them a sellout. So she makes a band and calls it "U stink." Then they play in a front of a crowd and the Backstreet Boys themselves come[0]. That episode and the ones where they have different animation like South Park and beavis and butthead were the ones that stuck with me as a kid. But I have to admit how long this aired, I thought it would end in 2015, but apparently they kept making new episodes.
[0] - https://youtu.be/F3x72g-s_bk