I agree.
Using pre-movie episodes as an example, just my opinion...
"Pressure" is, overall, a pretty solid episode. It's got good message, has some funny jokes, and plays with its own medium (animation) in a pretty funny way. It has one really horrible scene- in which Spongebob and his friends taunt Sandy as she's drowning and struggling for air.
"I'm With Stupid" is a pretty solid episode, too. It's funny and really memorable. Patrick is being a jerk, but the rest of the episode is so funny that I don't care.
"Born Again Krabs" and "Krabby Land" are both episodes I hate. They both contain really grossly cruel scenes (ie, Krabs selling Spongebob's soul to Satan, and Krabs mocking a brutally injured Spongebob,) and the episodes aren't funny enough for me to overlook or forget about those horrible scenes. I feel the same way about "The Great Snail Race," which is actually a lot worse, because A) the cruelty is part of the plot, and B) the message is handled so un-tactfully and is so grossly out-of-character.
just my thoughts...