Most of the ones I dislike are from Season 4:
Patrick SmartPants. That is the single worst episode of SpongeBob ever written. It had a great plot: Patrick becoming smart would make a great episode. But, because the new writers write like n00b fanfic writers, it turned out horribly. There wasn't anything funny about it, except MAYBE when Squidward had all the slobber on his clarinet. Other than that, I've never seen a dumber episode of the show.
BTW, second place goes to Dunces and Dragons. Another one that had an okay plot but turned out bad.