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.
Genius Bonus: Wayside School is Falling Down states that Albert Einstein didn't wear socks with the implication that socks make you less smart. It seems like an example of the books nonsensical humor but Einstein did prefer not to wear socks.
They Changed It, Now It Sucks: What some readers said after reprints of the books received illustrations that looked more abstract than those used from the 1970s through the '90s.
Toy Ship: The books are full of them. Jason and Allison is probably the most prominent but others include: Paul and Leslie, Dana and John, Calvin and Bebe, DJ and Kathy, Terrence and Rondi, Ron and Deedee, and Todd and Joy. A possible canon example is Mac and Nancy, a girl from another class. She's his friend in the first book but is said to be his girlfriend in the second. It's unknown if that's meant in a romantic sense but she does carry his books.
In Sideways Arithmetic from Wayside School, Word of God confirms that Jason and Allison are secretly in love with each other.
The Woobie: Miss Zarves in Gets a Little Stranger, in which she is upset over being unnoticed by the rest of the school despite loving her job and students.
Allison definitely needed a hug when everyone stopped noticing her, until she got to the nineteenth story.
Miss Nogard. Seeing as she gave up on all love and joy, can you blame her? In her introduction story, the way her heart was utterly shattered was outright tragic. She's more a victim if anything.