Charlie: I have often reread my progress reports and seen the illiteracy, the childish naiveté, the mind of low intelligence peering from a dark room, through a keyhole, at the dazzling light outside. I see that even in my dullness that I knew I was inferior, and that other people had something I lacked - something denied me. In my mental blindness, I thought it was somehow connected to the ability to read and write, and I was sure that if I could get those skills I would automatically have intelligence too.
Charlie's Nov. 16th entry near the end (July 25th in the short story):
Please... please... dont let me forget how to reed and rite...
The exact moment when Charlie's writing shows his decline, and he realizes what is happening to him reduced her to tears. Ditto for every time he mentions his coworkers in a positive light.
Pretty much every memory from Charlie's childhood.
The ending. When a character, regardless of their track record, does something inherently wrong, he or she should be punished accordingly. Charlie, who'd been basically slapped around like a bitch for the entire novel, lost the intelligence he'd wanted so badly, and was on his way to the mental institution he swore he'd never go to. The real kick in the balls is he did nothing to deserve this. He was a mentally retarded man who yearned to be "normal", and apparently that was too much to ask. Apparently that justified putting him through hell.
Knowing the final fate of Charlie, given that Algernon died, you know what's bound to happen...
There is a specially written version of the book that was suppose to look as if the Progress Reports were actually handwritten by Charlie. The chicken scratch scrawl from the start of the book slowly improved as the story progressed, and Charlie's spelling also improved as well. But take a look at the end and the last sentence.
"p.p.s. please if you get a chanse put some flowrs on Algernons grave in thebakyard..."
At the end of the sentence, a long, messy line trailed off of the "D" and moved off of the page, indicating that Charlie died while he was writing his last request, which was for someone to simply remember the simple pet rat who was the only thing that he could relate to. However, on other copies of the book, extra pages after this request are deliberately left blink, implying that Charlie had regressed to the point of extreme illiteracy instead of death.
One that stands out is when Charlie, after having lost his intelligence, returns to his old class with Alice just like he used to. He can't understand why she becomes so upset to see him there (at first); at that point, to him, it's just part of his routine again.