These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Muppets from Space
Big Lipped Alligator Moment: The "Celebration" song sung by the aliens when they finally show up. Of course, given that they are just as bizarre as Gonzo himself, it is perfectly in character. But the entire plot comes to a halt for the duration of the song.
The fact that the Muppets apparently start their day with a somewhat choreographed dance routine featuring the song "Brick House" may also qualify.
Critical Dissonance: Everybody complains about this movie. Of all the Muppet movies to date, this is the one that everybody claims to be the worst.
One, for the movie's entire premise. Gonzo's alien heritage was hinted at as far back as the first Muppet film, when he sang "I'm Going To Go Back There Someday."
As a child Gonzo did have vague memories of life on an alien planet, and being sent to Earth, if he did embellish a bit with his four-year-old imagination.
Gonzo's entry on the Muppet Wiki lists several other instances throughout the run of the Muppet Show and the rest of the franchise where he was involved in skits and songs relating to aliens.
...And some more Fridge Brilliance for Gonzo in general, during the lobotomy scene. Why is Gonzo so afraid of having his brain sucked out? The Gonzo we know performs death-defying stunts for a living and a hobby, views near-death experiences as adventures, and enjoys pain. Two possibilities:
He fears dying in a hospital (or a lab), in a bed, instead of going out with a bang during some exciting stunt.
He wasn't afraid of dying at all: he was afraid of losing his brain. Note that when Ed tells Gonzo his fate, Gonzo protests "but I need my brain!" He doesn't beg for his life, just his brain. Gonzo values his ability to think. Though weird, he's a very educated Whatever (most clearly seen in A Muppet Christmas Carol). And besides, without his brain, he won't be able to concoct his unique stunts anymore.
Tear Jerker: The end where Gonzo almost leaves with the aliens.
There's a moment early on where Gonzo looks at pictures of housemates with their family members (Kermit with Robin, Miss Piggy with her nephews, Fozzie with his mother) and then at a picture of himself, which shows him to be completely alone.
Gonzo's dream in the opening.
The Woobie: Gonzo, between his longing to have a family and his determination in the face of skeptics that he's an alien.