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.
Hilarious in Hindsight: In "Ice Cream Soup," Captain Carl is lost at sea, prompting Conky and Magic Screen to help him. They eerily foreshadow a modern car's GPS unit in the process—Conky explicitly uses a "satellite tracking device!"
While reading off a Chinese pen pal's letter in one episode, Pee-Wee excitedly says "I know Kung Fu!" Look again at who played Cowboy Curtis to see why this is funny.
Ho Yay: All over, but particularly Jambi, who John Paragon said he played as a "dishy gay man."
Mis-blamed: Contrary to popular belief, Paul Reubens' indecent exposure arrest in a Florida porno theater didn't get the show cancelled (though it did get his merchandise recalled, the reruns CBS was airing had to be taken off due to the incident, and he became a punchline to many a dirty joke both on TVnote cf. In Living Color!'s "Pee Wee's Mugshot Doll and Pornhouse Playset" sketch on the first episode of season three and in real life). Reubens chose to end the show as he didn't want it to go stale from staying on the air for too long and he wanted to branch out and do other things.
Nightmare Fuel: If you caught it on [adult swim], you might find it more nightmarish than whimsical (of course, if this show scared you as a kid, it might trigger you in adulthood).
Pee-wee's toy shelf from Season 1 was in a class all its own, combining creepy stop-motion, surreal claymation and ghastly patchwork abominations into a single big circle on the Venn diagram of things that freaked kids out in the 80's. It's not hard to guess why Clocky replaced it on the Playhouse wall for the rest of the show.
The horrific, dead-eyed Salesman also disappeared after Season 1 for the same reason.
Pee-wee got his very own talking doll when the show was in its heyday. It wasn't the usual Creepy Doll, but it took a turn for the worse when you pulled the string: his trademark scream was rendered as the doll roaring at you.
Special Effect Failure: The show had some very painful Chroma Key throughout its run. It's most obvious in "Luau for Two," when Pee-Wee does a limbo move—he literally becomes a 2-dimensional figure!
What Do You Mean, It Wasn't Made on Drugs?: Wayne White, who helped create the set and several puppets and provided the voice and puppeteering for Randy (who he also made) admitted that marijuana was a big part of the creative process for the show, though the show's aesthetic is supposed to be based on live-action 1950s kids' shows with bright colors and loud, energetic hosts.