I really enjoyed the first half of Season 3, but the second half is where it all started to go downhill in my opinion. Most say it went started going downhill in Seasons 4 or 5 (Pretty okay Seasons IMO), but I think that the latter half of Season 3 was showing signs of the crew "losing steam" so to speak. This will be a long entry.
This half of Season 3 also established overly-greedy Mr. Krabs in Born Again Krabs, and Krabby Land (A very late season 3 episode). Did we get greedy Mr. Krabs before those episodes? Oh yes, especially Jellyfish Hunter, but that episode made it very clear he was meant to be the antgonist, unlike those two episodes. SpongeBob also had the tendency to be a jerk, either because his pet snail did not want to compete in a race (The Great Snail Race), or because people aren't following his lame party rules (Party Pooper Pants). He also acts pretty dumb in general in the latter half of S3, sure there are episodes that he acts somewhat intellegent in, but still. Patrick didn't get too much of a downgrade thankfully, the worst he does is spary SpongeBob with Invisible Spray and pretty much haunt Bikini Bottom along with SpongeBob in Pranks a Lot, the very last Season 3 episode, and the last pre-first movie episode. One last issue, the 2nd half feels... off. IDK, eveything from the animation, to the general feeling, it's off. You could definitely tell they were making a switch to Season 4.
I do think Season 3 of SpongeBob is really good overall, but I could live without most of the epiosdes in the second half of the season.