I find SpongeBob You're Fired to be one of the worst, if not, the worst episode of the entire series. The plot is absolutely formulaic and boring, plus the jokes are really unfunny. I also find The Clash of Triton quite bad, although there's some intrigue regarding the flashbacks and Bob and Pat's heroic act of freeing the party goers. WhoBob WhatPants is terrible, as it suffers from the same problems with You're Fired (although the art slightly makes up for that), and lots of missed potential. Only fascinating scene involves SpongeBob and the Bubble Poppin' Guys chasing the former. Have You Seen This Snail? is meh, although the Gary Come Home song is definitely the special's highlight.
I have a soft spot for SpongeBob vs. The Big One (titled SpongeBob and the Big Wave overseas) because of the interesting subplots and how the main story is developed (it's also funny, although it doesn't have that many laughs), and I love the Great Patty Caper, Friend or Foe, It's a SpongeBob Christmas, Dunces and Dragons, Christmas Who? and Last Stand specials. Party Pooper Pants, Ugh, The Sponge Who Could Fly and Goodbye Krabby Patty? also have great jokes (don't forget to listen to the amazing When Worlds Collide and Underwater Sun songs), but aren't as exciting story-wise.
Atlantis SquarePants is boring (let aside one or two jokes with Mr. Krabs running a fake entrance cash desk and SpongeBob allegedly talking about how much Gary needs him in order to leave Atlantis at the wake of breaking the oldest-living bubble) and the songs are meh (only two that stand out for me are The Bubble Song, which is pretty niche out of context, and the emotional Goodbye Atlantis song. Also, Sandy's Song and Plankton's Song are accompanied by nice visual art and 8-bit animation, respectively). The Patchy segments are really good, but it all comes down when these weird puppet aliens appear. Truth or Square is pretty interesting in retrospect as a nice little parody of anniversary specials, but doesn't have much going for it otherwise; the songs are really good, and the Patchy segments that didn't make it to international runs are frankly awful. Big Birthday Blowout was really good and showcases well the pros of the latest Vincent Waller era episodes (great imagination, funny and inventive jokes, and pushing the boundaries overall).
There's also Pest of the West; it's the most forgettable SpongeBob special in my opinion. Unimpressive story, unimpressive (and unfunny) climax, unimpressive humor, unimpressive everything. The art style doesn't do much to save this mess.
...best things about the SpongeBob specials are the art styles and the music.
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