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. It's extremely HEARTBREAKING seeing how realistically the Chipmunks reacted to this situation. 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.
To top it all off, the fact that it's ALVIN... the one Chipmunk that is usually a troublemaker and thinks he is the greatest... actually CRYING over losing the poor kitten, can easily cause your eyes to water up.
Additionally, the episode was based off a real-life experience, when Ross Bagdasarian Jr. and his wife Janice Kraman's dog Tiger Lily was killed by a car. The Chipmunks' new puppy Lily was named after her.
The Chipettes' origin story episode.
Also when the Chipettes become Miss Miller's adoptive daughters.
The Chipmunks meeting up with Vinnie, their Missing Mom in the special "A Chipmunk Reunion".
Other tearjerkers of the special include Vinnie explaining that she really wanted to keep them but truly had no choice, Alvin trying to call them out he felt her absence the most and then running away with his brothers on tow, the Chipmunks being attacked by a wild moose and, after Winnie saves them, thinking she's dead.
The It's a Wonderful Plot episode "Dave's Wonderful Life" which has a stressed Dave suffering from financial problems, as his recent songs were rejected. It's hard to feel bad for him when he laments over his problems before going to bed.
Also, the fates of the three Chipmunks without Dave: Simon is still in kindergarten at the age of 40 because he failed in a spelling bee contest and lost his self-confidence, Theodore becomes a hermit, and Alvin is struggling in a dead-end job.
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. (Alvin slumps; As Brittany begins to leave, she turns around) 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.
Brittany: You do? Why?
Alvin: 'Cause he's not even looking.
Brittany: 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....
Jeanette getting kidnapped by Zoe and then forced to bring her the treasure. Jeanette's singing doesn't help.
Jeanette: S.O.S. Please,someone help me. It's not healthy for me to feel this...
For Road Chip:
When Alvin explains the whole reason they left the house to Dave and return the engagement ring to him. Then it turns out Dave was never gonna propose to Samantha; the ring the Chipmunks stole was actually for his friend Barry's proposal to Alice. In place of the ring, the box has a breath mint, and Alice storms off, insulted. What sells it most is the extremely guilty look on Alvin's face as he realizes he really screwed up this time.
Right afterwards, Dave scolds the Chipmunks in the hotel room.
Dave: Look, the only reason we're not going back to L.A. right now is 'cause I have to be here. (sighs) I don't think I've ever been more disappointed in you boys than I am right now. (leaves and closes the door behind him) Simon: If Dave didn't wanna get rid of us before, he definitely does now.