There are a number, but how Matron passes out, and Patrick's later imitation of it, rank high up there.
In the first book, Omri's brother Adiel accuses him of stealing his gym shorts, and they practically get into a fistfight over it. But then:
"Are these them?" asked a small voice in the background.
Omri and Adiel turned. Patrick was lifting up a crumpled navy-blue object from behind a radiator.
Omri felt the anger go out of Adiel.
And Adiel is so embarrassed that he even helps Omri to his feet.
When Boone (who appears to be quite obviously hungover) stumbles out of the titular magic cupboard, unaware that he'd been transported through time and space (and size). After swearing to lay off the hooch several times in a row, he realizes that he's surrounded by giant children.
A mild example, but there's one scene with Little Bear building his longhouse while Omri's away at school, singing in his native language as he works. Suddenly, from off screen, we hear the sounds of hammering (presumably Omri's father building the skylight that A.D. wanted.) and Little Bear suddenly goes quiet, listening. After a few moments, he decides whatever he's hearing isn't a threat to himself and starts singing again.
There's a brief all-out battle between Darth Vader, the T-Rex from Jurassic Park, RoboCop, a Ferengi and a few others. A second later they all pause to take in what's going on and look up at a very freaked out Omri.