I would want to pick quotes that are relevant to the central themes of the story and help us to understand those themes more clearly. So, as one of the central themes is manipulation and the way in which Ender is manipulated amongst others, I would firstly choose the following quote:
He held up a limp hand. "See the strings?"
Ender here shows his imaginary "strings" to his sister when visiting her on earth, which obviously indicates the way that he realises he is being manipulated, even though he might not be aware of the depth of that manipulation.
Another aspect of this novel is the competition that rages throughout it. Under the guise of a "game," wars are fought and casualities, real and fake, are made. Consider this quote:
The message was clear. Winning is more important than anything.
As Ender tries to make sense of his new world in the training academy, the one lesson that comes through loud and clear is the way in which winning is so important.
Lastly, you may want to think about this quote, which is about freedom and confinement:
Human beings are free except when humanity needs them.
This is what Graff says when talking about the limits of human freedom. This book raises fascinating questions about whether we are free and to what extent we can consider ourselves to be free.