Ah, desks. We've all spent many an hour sitting in one, watching the second hand of the clock tick slowly around, gazing at the classroom map, and planning the easiest way to get from campus to a Tahitian beach. (We're also uncomfortably touched the used gum of some monster who thought it would be a good idea to stick it there.)
Yeah. School desks aren't the most relaxing of places…and they're usually not the most interesting.
And that's also how Welton students seem to feel. When we see their first day of class, special attention is paid to the desks that confine them. They sprawl, uncomfortable and antsy. Just a shot before, they are shown rushing down the stairs and exclaiming loudly. This contrasts reminds the viewer just how restricted and bored the boys are when confined to their desks. Desks are definitely a symbol of repression in the film.
So when Mr. Keating forces the students to leave their desks behind during the first few minutes of class, the students seem as shocked as a cat confronted by a cucumber. He's trying to break them from their status quo. Later, when Mr. Keating has them stand on his desk, they seem even more shocked. He's trying to get them to look at life from a different point of view.
And how does he do that? By having them treat desks, the symbol of confinement and repression, in a new way. It's no coincidence, then, that in the final scene they stand on their desks of their own accord. By literally standing on the symbol of their repression, the boys are truly breaking free.