"Journey's End" had one of the warmest moments in the show's history when the Whiskers adopted that Zappa pup... but then it had the moment that shattered the show, in the death of Flower. Especially knowing that Next Generation isn't as good, Rocket Dog has lost the might of the Whiskers.
Shakespeare, always nice and caring with the pups, dying in the act of defending them against Big Cy from the rivalling group.
The 2nd-to-last episode in the same season ends with the death of Mozart, who had been in Woobie territory for the entire series up until now. To make it worse, the episode seemed to show that she might have still had a chance for a happy ending, right before crushing it in the last few minutes. Really, season three was riddled with tearjerkers, with the loss of so many meerkats.