People are Inherently Good
Sideways Stories from Wayside School's story is an allegory which conveys that most people are inherently good. Each character in Sachar's book is, despite some of their bad acts, a good person who acts out out of pure maliciousness. Todd, for example, acts out fairly frequently in Mrs. Jewls' class but does not do so out of maliciousness.
Authority is Sometimes Stifling
Sideways Stories from Wayside School's story is an allegory which conveys that authority can be stifling. The kids in the novel, many of whom act out in rather significant ways, are not deterred by their teachers, who often work to quash their students' vivaciousness and creativity. For example, the students in Mrs. Jewls' class are not deterred by some of the strange rules that she sets out for them.
Crazy Things that Kids Do
A common motif in Sideways Stories from Wayside School- and in the Wayside School series as a whole - involves kids doing crazy things to have fun (like Bebe's drawing competition). Sachar includes this to emphasize how wacky and zany his book and the characters in it are.
Strange Behavior by Adults
A fairly common motif in Sideways Stories from Wayside School is the strange behavior of many of the adults in the novel (like Mrs. Jewls thinking that her class was made up of monkeys). Sachar includes this motif in his novel as a way to emphasize how excellent and unique the children in the novel really are.
Chalkboard
The chalkboards in the classrooms are symbolic of the order and discipline that the teachers force their students to abide by.