The episode "Cookie Chomper III" Oh God, easily the biggest tearjerker of the show. An adorable stray kitten sneaks through a window into the house and the chipmunks adopt him. Dave even overcomes his allergy to cats and accepts the new pet. One night, the kitten wanders out through an open window in the chipmunks' bedroom and is hit by a car. Theodore is incredibly upset, Simon is too miserable to do anything, even Alvin is saddened by the whole thing, going as far as removing the live plants from the house so they don't die.
The Chipettes' origin story episode.
Also when the Chipettes become Miss Miller's adoptive daughters.
The Chipmunks meeting up with Vinnie, their Missing Mom.
For 2007 Alvin and the Chipmunks film with Jason Lee:
For The Squeakquel:
When Alvin fails to arrive at the sing-off due to a football game, thus giving the Chipettes a victory that they are not proud of. When he finally arrives, the auditorium's empty and Brittany calls him out on his selfishness before leaving. When Alvin arrives home, his brothers pretend to be asleep and ignore him.
Brittany: You know what, Alvin? Ian was right. You don't care about anyone but yourself. Oh, and by the way, I never wanted to win this way. (leaves, the auditorium's lights go out on Alvin)