The episode "Cookie Chomper III". Oh God, easily the biggest tear jerker 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 (to the point where he's in denial of Cookie's death), 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 the family doesn't have to deal with any more death. He even yells at their neighbor for walking her dog across their house, saying that he won't allow any living beings here. The neighbor and the dog look confused and upset upon hearing this.
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:
The Third-Act Misunderstanding when the chipmunks find the goodbye letter Dave had written for them earlier in the movie. Since they find it after he angrily suggested that they go live with Ian if he was treating them so much better, they assume he still feels that way and really does want them gone.
Simon:(Reading the letter with the others) '...You should go back to your real home in the forest.;...I guess he really does want us to go.
Later on, when they realize just how unhappy they are working with Ian and want to go home to Dave, but thanks to Ian's manipulation, they're convinced Dave doesn't want them back.
Theodore: Guys....I wanna go home.
Simon: What do you mean? You are home.
Theodore: No, I mean home home. You know, with Dave.
Alvin: But, Theodore, come on. Wake up and smell the toffee. Dave...doesn't even want us. He doesn't care enough to even come to our show....
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)
Alvin's Jerkass Realization and his assumption that he's why they haven't been found by Dave yet.
Alvin: Brit, I...I think I know why Dave hasn't come.
Brittney: You do? Why?
Alvin: 'Cause he's not even looking.
Brittney: Alvin, why wouldn't he be looking for us?
Alvin:Because I drive him crazy. You know, the way Simon's been driving me crazy? I mean, that's what I've been doing to Dave. For years. No wonder he hates me....