"Pathfinder," The ending when Reginald Barclay at Starfleet Communications on Earth, successfully makes contact with the lost USS Voyager. With a quick data exchange and welcome words of encouragement from Admiral Paris, the time of Voyager's total isolation from home is over with the knowledge that the crew will have the help of their comrades in the Alpha Quadrant from now on. Particularly Admiral Paris telling his son Tom that he misses him, and is proud. On Earth, the Admiral and Barclay agree that the first objective of Project Pathfinder has succeeded and now it's time to help the lost ship get home.
Admiral Paris: How are your people holding up? Janeway: Very well. They're an exemplary crew, your son included. Admiral Paris: Tell him... Tell him I miss him. And I'm proud of him. Janeway: He heard you, Admiral.
While throwing a party to celebrate the achievement, the crew of Voyager makes Reg an honorary crew member.
Tom: To my dad. It's nice to know he's still there. And to the newest member of the Voyager family, Reginald Barclay... whoever you are. (everyone raises their glasses) Janeway: Here here! To Mr. Barclay!
The look on Tom's face when he first hears his father's voice is especially great.
After the transmission cuts out:
Harkins: You did it, Reg. I'm sorry I doubted you. Admiral Paris: Why the long face, Mr. Barclay? Barclay: Because it's over, sir. Admiral Paris: No, Lieutenant. I'd say that Project: Voyager is just beginning. Thanks to you.
Also, the last part of "Message in a Bottle" after The Doctor returned to Voyager and relayed Starfleet's message, especially the last two sentences:
The Doctor: And they asked me to relay a message: they wanted you to know you're no longer alone. Janeway: Sixty thousand light years seems a little closer today.
Quite impressive considering the humor in the episode. Had it not been so well-carried-off, it would have felt like Mood Whiplash.
Last part of "Timeless", when Janeway talks to Harry and Harry sees his alternate self's message.
"The Chute." A prison mob wants to beat up Tom. Harry stands up for his wounded comrade, only to later beat Tom savagely for destroying what Harry thought was their only way of escape. Later after they are rescued, Harry comes to apologize for nearly killing him.
Tom: You want to know what I remember? Someone saying, 'This man is my friend. Nobody touches him.' I'll remember that for a long time.
"Night." Captain Janeway instructing the crew to leave her behind so she can blow up the evil corporation's route to its' environmentally-unsound waste dumping ground and still allow Voyager to shave two years off their return trip, then every single member of the bridge crew refusing her orders to drop her off and keep going (especially when Janeway turns to Seven, who says "I will not comply" before Janeway opens her mouth).
The ending of "Night" was another one. After travelling for months through a soul-crushingly empty, starless void, one lonely star appears on the viewscreen. Then another. And another. And then...◊
B'elanna(Just before they initiate their plan to escape the void): See you on the other side.
"One Small Step". The whole episode (or most of it), especially Seven's speech.
In particular, I loved that Seven had evolved as an individual enough to notice John Kelley's final wish: to know who won the World Series. She even cared enough to whisper the final result to his coffin. If she had had this experience even a year before, one wonders if she would have noticed or cared about such "irrelevant minutiae" as the World Series.
And for the record: "The Yankees, in six games."
And then Tom gives the greatest smile. He's the history buff, and he understands.
In the season two premiere "The 37's", Voyager finds a Human settlement of about 100,000, descended from humans kidnapped from Earth in 1937 (including Amelia Earhart) and comes to the conclusion that returning to Earth just might be a lost cause and she has no right to force her crew into such a dangerous and difficult undertaking. She announces that if anyone wants to stay on the planet, they should report to the cargo bay the following day. Tomorrow comes, and Janeway enters the cargo bay...to find it completely empty. Her face is a Crowning Moment of Heartwarming just by itself.
The end of "Riddles", from season six. After getting shot and suffering brain damage, Tuvok becomes completely unlike himself and starts to enjoy things like jazz and cooking, as well as bonding with Neelix. When they find a way to cure him, he doesn't want to go back to the way he was, but Neelix convinces him.
Tuvok: But how will you know how much I enjoy being with you? Neelix: You just told me.
The scene in "Homestead" when Tuvok dances for Neelix gets this troper every time.
"Author, Author" had a short but great one. When Voyager gets its first visual link with the Alpha Quadrant, Barclay relays them a live image of Earth.
The second part of 'Year of Hell' had a very touching one. When Janeway sends her senior officers to the ships of her allies in preparation for the attack against Annorax, Tuvok stays behind to object. She refuses to leave with them, telling him the captain goes down with the ship. He understands, gives her the Vulcan salute (Live long and prosper) and she returns the sentiment - "Same to you, old friend." Finally, she hugs him one last time, knowing he won't return it, but wanting to express her feelings all the same. AND THEN HE RETURNS IT. Vulcans don't always get human emotions, but Tuvok understands at least one: affection.
Also in "Year of Hell" you have Seven of Nine. After Tuvok was blinded saving Seven from an explosion, Seven acts as his eyes, assisting him through the ship and even offering to help him shave. The conversations they have hint that the reason she is doing this is becoming less out of gratitude/guilt and more out of a growing sense of friendship between the two.
This, from "Resolutions" :
Chakotay: It's about an angry warrior who lived his life in conflict with the rest of his tribe. A man who couldn't find peace, even with the help of his spirit guide. For years, he struggled with his discontent. But the only satisfaction he ever got came when he was in battle. This made him a hero among his tribe, but the warrior still longed for peace within himself. One day he and his war party were captured by a neighbouring tribe led by a woman warrior. She called on him to join her because her tribe was too small and weak to defend itself from all its enemies. The woman warrior was brave and beautiful and very wise. The angry warrior swore to himself that he would stay by her side, doing whatever he could to make her burden lighter. From that point on, her needs would come first. And in that way, the warrior began to know the true meaning of peace.
Janeway: Is that really an ancient legend?
Chakotay: No, but it made it easier to say.
"Lifesigns", in which the Doctor first experiences love... with a nice Vidiian doctor. He had given her a holographic form with a healthy appearance to keep her alive, and she was grateful to experience a "body" without the disease, but afraid to go back to her diseased corporeal body. But at the end, it is that body that he has his first dance with—it was never her appearance he cared about.
Janeway: I'm putting you on report, in case that means anything anymore. Chakotay: It means something to me, Captain. It means I've let you down ...and for that I'm truly sorry.
The scene near the end of "The Voyager Conspiracy" how Janeway convinces Seven to come back to Voyager.
In "Dreadnought" when Captain Janeway tells the leader of the planet the titular missile is heading towards she'll use Voyager to stop the missile at the expense of her own ship and the lives of everyone on board. Pretty much the first time someone has appreciated Voyager since its arrival in the Delta Quadrant, mostly because the Kazon were spreading vicious rumors about it.
Kellan: You would sacrifice yourselves to save a people you didn't know two days ago?
Janeway: To save two million lives? That's not a hard decision.
Kellan: Your reputation in this quadrant isn't deserved, Captain. For what it's worth... you have made a friend here.
The fact that Seven is the crewmember who takes Naomi under her wing. Yes, Neelix tries his best to be a wacky uncle, and the writers apparently forgot that Samantha Wildman survived her injuries in her last appearance, but it is Seven that makes a real connection with the girl, and vice-versa.
In "Once Upon a Time," when Tuvok and Samantha Wildman are stuck in a shuttlepod together and Wildman is afraid she might die, leaving her daughter essentially orphaned. Tuvok gives her a completely Vulcan-logical speech to calm her down, essentially reassuring her that even if the worst does happen, she can rest in the knowledge that she did her best to raise her daughter right.
In "Death Wish," the rebellious Q (Quinn) seeks asylum on Voyager. He wants to commit suicide, feeling his life is meaningless and that death would create a new discussion in the Continuum. A trial results, with the John de Lancie Q arguing on the Continuum's behalf to re-imprison Quinn. When Janeway rules in Quinn's favor, he is Brought Down to Normal and made human. He dies not long afterwards from poisonous hemlock - something he couldn't have gotten on his own. It turns out that Q gave it to him to help him with the one thing he wanted most.
"By demanding to end his life, he taught me a little something about my own. He was right when he said the Continuum scared me back in line. I didn't have his courage or his convictions. He called me irrepressible. This was a man who was truly irrepressible. I only hope I make a worthy student."
Sulu: You'll find that more happens on the bridge of a starship than just carrying out orders and observing regulations. There is a sense of loyalty to the men and women you serve with; a sense of family. Those two men on trial... I served with them for a long time. I owe them my life a dozen times over. And right now they're in trouble, and I'm going to help them; let the regulations be damned. Tuvok: Sir, that is a most illogical line of reasoning. Sulu: You better believe it. Helm, engage!
"The Fight" has a couple.
Harry Kim (in Chakotay's hallucination) telling the commander that he's his role model.
When Chakotay is babbling nonsense, clearly hallucinating, and tells Janeway, "...he's got a few kilowatts on me, a few centimeters in height, but I can take him Captain!" His tone of voice suggest he wants to do it for her and the crew. There's something heartwarming about the fact that even when he's too delusional to tell up from down, Chakotay still wants to serve Janeway and the crew.
In "Day of Honor," when Neelix invites B'Elanna to use him as a verbal punching bag, as a solution to her rages, and B'Elanna rejects the offer. The fact that she can lash out at her captain, her oldest friends, and her lover, but just has too much of a soft spot for Neelix, the most peaceful person on the ship...is odd, but oddly believable, and touching.
The entirety of "Drone" from beginning to end. That a ridiculously overpowered Borg drone from the 29th century can be made adorable is a true feat of productionnote none of which should be attributed to the writers who have a habit of accidentally falling into good stories rather than writing them. The fact that by the end of the episode the loss of "One" is enough to cause a genuine tearjearker in-universe for Seven and the rest of the crew that get to know him, only drives it home.
B'Elanna: Maybe this is the collective's new strategy. They don't assimilate any more they just show up and look helpless.
The "message from Starfleet" subplot from the episode "Hunters". Starting with the crew receiving a garbled message from that, when cleaned up, is far less professional and much more personal than they expected, to realizing that the "message" was actually letters, to the distribution of the letters as they're received and deciphered.
In "Scorpion," Janeway struggles with the choice between pushing on into Borg space to get home and risking assimilation, or turning the ship around and asking her crew to live out their lives in the Delta Quadrant.
Janeway: I keep looking to all these captains—my comrades in arms. But the truth is, I'm alone. Chakotay: If that moment comes, we'll face it together, and we'll make the right decision. You're not alone, Kathryn. Janeway: Three years ago, I didn't even know your name. Today I can't imagine a day without you.
At the end of "Endgame", Where after seven years, Voyager finally gets home.
The look on Tom's face when he hears his newborn daughter over the comm.
The last line of the series — Janeway softly echoing her order "Set a course ... for home." — is the same as in the first episode, (part two of the series opener "Caretaker").
Harry's speech, as the crew debates whether taking the opportunity to go home or dealing a serious blow to the Borg Collective:
"I think it's safe to say no one on this crew has been more... obsessed with getting home than I have. But when I think about everything we've been through together, maybe it's not the destination that matters; maybe it's the journey. And if that journey takes a little longer, so we can do something we all believe in, I can't think of any place I'd rather be or any people I'd rather be with."
The end of "The Q and the Grey," where Q is playing with his newborn son. Quite the turnaround from someone who once described babies as "squirming little infants" on TNG.
"By the way, did I tell you how smart he is? I've already taught him how to knock small planets out of orbit."
In "Tinker Tenor Doctor Spy," the crew have to view the Doctor's fantasies on the holodeck, in order to help fix the malfunction with his experimental daydreaming subroutines. Most of it is simple wish fulfillment. The Doctor being an action hero and getting all the girls. But just as they're leaving the holodeck, a new scene comes up that makes Janeway pause to watch. The dream version of herself is congratulating the Doctor on some sort of metal she's just presented him. To which he responds:
"Thank you for this opportunity, Captain. All I've ever wanted was to live up to my full potential, to hone all my skills, expand my abilities, to help the people I love."