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.