I can only think of a few.
Squeaky Boots - Actually a pretty decent episode, but the squeaking can get really annoying and Mr. Krabs was a little out of line in this episode.
SpongeBob B.C. (aka Ugh) - "Ugh" pretty much sums up this episode. This felt like Stephen Hillenburg got into a time machine and brought a season 6 episode back into season 3. This episode barely had a plot and having the characters just talk gibberish for an entire episode got really irritating.
The Camping Episode - Another episode that felt like a later season episode got sent back. This episode started the "Squidward Gets Tortured" gags that would later be overused and the joke about a dirt circle stopping a bear had a similar vibe to some of the unfunny awkward gags from the latter day episodes.