The chipmunks and Dave placing the collar of their dead kitten on a plaque. It reads "In loving memory of Cookie Chomper III".
The end of that episode would qualify as well.
The chipmunks being reunited with their real mother.
"The Wall", the Chipmunks sing a song called 'Let The Wall Come Down' and through the Power of Rock and Power of Love bring the Berlin Wall down.
Fridge Brilliance: This aired the wall actually came down. Alvin said "it was all just a dream, but it doesn't have to be." Eleven months later...dream became a reality.
The end of the episode where Dave dreams about what The Chipmunks would be like without him around. It ends with a wonderful song that shows just how grateful they are to have him. Could also qualify as a tearjerker.
The episode "Sisters" has at least a couple of nice little heartwarming moments, both of which involving Brittany realizing how she mistreated Jeanette:
One of which where Brittany realizes she broke her promise to meet with Jeanette and the pig they're caring for for science class in the park; she comes home to find them asleep on the couch, walks over and gives both of them a kiss on the cheek.
Finally when Brittany is heartbroken over not being accepted in the Sister clique, so Jeanette presents her with a large bouquet of roses.
Brittany: But, Jeanette... I was so awful to you.
Jeanette: You're my sister, Brittany, and real sisters stick together.
Brittany: (Tears; hugs Jeanette) You're the best, Jeanette!