When Niles finds out she is having an affair with their marriage counselor he is heartbroken and he realizes it's the end for them.
"And then I ran into the bedroom, tears pouring down my face and said 'Mommy, mommy! The puppy Santa gave me for Christmas won't wake up!'" (From a caller to Frasier's radio show in Season 1's "Miracle on Third or Fourth Street".)
Given the sheer bombardment of Christmas-themed misery Frasier and Roz have suffered by that point, this one also has Black Comedy points.
In the final episode, when Niles said, "I'll miss the coffees."
A subtler example moments before; when the removal man comes to take Martin's chair away, Frasier expresses relief at finally getting it out of his apartment, but can't resist telling the guy to make sure he takes care of it. Then, once he's moved his preferred chair into its place, it seems to finally sink in that he's all alone.
When Frasier recites the Tennyson poem.
The final few moments of the finale can bring tears to your eyes. Especially when you realize that Frasier's farewell message to his family, and later his radio listener, can just as well be taken as a direct message to the viewer.
In the episode "Frasier's Edge", Frasier's mentor, Dr. Tewksbury, is trying to help him through a crisis of confidence. He advises to diagnose himself as if he were a caller on his own show. Frasier tries to stall by bringing up numerous exercises, but Tewksbury pushes him to deal with his feelings. Finally, Frasier breaks down:
Frasier: But I don't know what he wants!
Dr. Tewksbury: Then why do you keep trying to bury him in psychiatric exercises?
Frasier:Because that's all I have!
[long pause, Tewksbury looks at him sadly]
Frasier (whispering): ...I'm sorry, caller. I can't help you.
That was the most depressing thing this troper ever saw on Live Action TV. It's heartbreaking.
And then at the end of that episode, when Frasier is given his Lifetime Achievement Award, he says to the crowd:
Frasier: Thank you for honoring my life...... I just wish I knew what to do with the rest of it......
In the Season 9 episode "Deathtrap," after Martin explains about "Hamster Heaven" to console Roz's daughter Alice about her dead pet, Alice asks about whether Eddie would be going to "Dog Heaven." Martin laughs and says not for a long time. But after she leaves, Martin looks somber and calls Eddie over to his lap for a hug. The look on his face as he realizes that Eddie won't be around forever made me tear up.
Reality Subtext: Moose, the dog who originally played Eddie, was retired from regular appearances at the end of the previous season. He was getting too old to perform some of the tricks so his son, Enzo, had taken over the role.
"Something Borrowed, Someone Blue": Even Frasier himself said "It just breaks my heart!" The scene where Niles and Daphne dance together, to the song "They Can't Take That Away from Me", aware that their chance to be together is slipping away forever...
In "Room Full of Heroes," Frasier hosts a costume party where everyone's supposed to dress as their own personal heroes. Niles comes as Martin, which at first is incredibly heartwarming. But as the night goes on, Niles takes the role farther and farther, sinking into it more and more, until in a moment of passion, he declares both his "sons" complete disappointments and utter failures. It's sad enough that, deep down, Niles thinks that's his father's real opinion, but the saddest thing of all is Martin's face on the verge of tears as he looks at Niles and says, so quietly, "You will not put those words in my mouth."
In the episode "Daphne Returns", Niles finally realises how deeply embedded in fantasy his infatuation with Daphne has been:
Frasier: You have a chance for a real relationship with Daphne, yet you're resisting it.
Niles: Why would I do that?
Frasier: Because if your relationship with Daphne doesn't work out... then you will have spent the last seven years of your life... chasing an illusion.
Frasier and Martin's talk about the infidelity of both their wives. Yes, Frasier's beloved mother cheated on his father.
In "A Day in May" one of the b-plots has Martin sitting at a table in a strange room drinking a cup of coffee. When Niles calls him he lies and says he's at the track. Later he's met there by a woman. While chatting they both say they think about each other a lot, and the woman asks how his hip is doing. An old flame of Martin's, perhaps? Not quite. They're at the local prison to attend the parole hearing of the woman's son. He was the criminal who shot Martin in the hip, cutting short his police career and crippling him for life. The young man describes his success with the prison work program and how he hopes to get a job in computer science once he gets out. And he says he regrets his crime "every day." The parole board asks Martin if he'd like the make a statement. Martin struggles to his feet, pauses for a moment...and says "I have nothing to say." The board ultimately decides not to grant parole. As Martin starts to leave the young man's mother quietly sobs in her seat. Martin turns around as if to comfort her...but he has nothing to say...
In "Our Father, Whose Art Ain't Heaven", Frasier, after lying about liking a painting Martin bought for him, finally decides to be honest with his father about not liking it. Martin seems to accept the explanation, but then breaks down into tears, devastated that his own son would accept a gift he didn't want. Seeing that he made his father cry makes him start crying too. While it's a funny scene in itself (see the "Funny" page), the fact is Martin seems to think he failed as a father ("I could never do anything for my sons") and Frasier is ashamed that he was so ungrateful and caused his father so much pain. Underneath the laughs, the scene's undercurrent is still heartbreaking.
At the end of the season premiere "Don Juan In Hell":
"In loving memory of our friends Lynn and David Angell"
(the executive producer and his wife, killed aboard the first plane to strike the World Trade Center during the 9/11 attacks, which had taken place only a few weeks earlier)
Roz ending up in tears about breaking up with her boyfriend, Roger. Both times.