From the moment that she comes aboard, Kes (though she definitely understands that he isn't flesh and blood) treats the Doctor like a person. The Starfleet crew and the Maquis and even Neelix mostly treat him like an inconvenient tool much of the time at this point, but she legitimately cares about the Doctor and respects him as an individual, to the point where, when the crew think they've found a way home for the crew but not the ship in "Eye of the Needle," she's the only one concerned about his fate.
"Caretaker": This is sweet coming from a Vulcan.
Janeway: I spoke to your family before I left. Tuvok: Are they well? Janeway: Well, but worried about you. Tuvok: That would not be an accurate perception, Captain. Vulcans do not worry. Janeway: They...miss you. Tuvok: ...As I do them.
In "Parallax", although B'Elanna is confident in her engineering ability, the circumstances under which she left Starfleet Academy left their mark on her, which is why she's surprised to learn something new about her time there.
Torres: I'm not officer material and we both know it. The truth is, I quit the Academy because...I realized I couldn't make it in Starfleet. And believe me, no one was sorry to see me go. Janeway: Professor Chapman was. Torres: What? Janeway: He put a letter in your permanent file, saying that, should you ever reapply, he would support you. He thought you were one of the most promising cadets he'd ever taught. Torres: I fought with him almost every day. I was always questioning his, his methods, his assumptions, and he was always slapping me down like some upstart kid. I was surprised he didn't help me pack my bags. Janeway: Some professors like students who challenge their assumptions, B'Elanna....And so do some captains. Professor Chapman wasn't alone. Many of your teachers thought you had the potential to be an outstanding officer. You had more friends at the Academy than you realized.
Also from "Parallax", B'Elanna and a previously skeptical Janeway geeking out together as they bounce ideas off of each other in the conference room. Never has a runaway freight train of Technobabble been so Adorkable.
In Phage, Kes tells the doctor hes been remarkable, and despite being a hologram, he can learn how to deal with emotions like the rest of them. He repays the favor, starting her training as a nurse. This continues in Eye Of The Needle, where she sees how badly everyone treats him, and doubles down on appreciating him, while hes proud of her curiosity.
Eudana helping out Kim by introducing him to someone with the technology that might be abel to get them home in Prime Factors.
From a certain point of view, the fact that the man illegally selling them the teleportation technology doesn't want anything sinister or overly luxurious, but merely Federation books to bring new entertainment to his people (albeit entertainment he can sell).
Even if it is disobeying the captains orders, seeing Federation and Maquis personal cooperating together to try and get the teleportation technology.
In "State Of Flux", the reveal that despite the circumstances of his Passed-Over Promotion, Carey hasn't been having any problems with Torres (although they can't be sure enough to avoid seeing him as a Red Herring suspect).
The same episode has Tuvok assuring Chakotay that it wasn't his fault that he didn't suspect the multiple spies, including Tuvok, onto his crew.
Paris and Tuvok's conversation at the end of "Ex Post Facto"
Paris: How come I always see you down here eating alone, Lieutenant? Tuvok: I prefer to read rather than engage in, what do humans call it? Short talk? Paris: Close enough. You don't make many friends that way. Tuvok: Perhaps. Paris: Well, like it or not, you've made one today, Mr. Tuvok.
"The 37's" has a very sweet ending. Voyager finds a Human settlement of about 100,000, descended from humans kidnapped from Earth in 1937 (including Amelia Earhart), and Janeway 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 she enters the cargo bay with Chakotay...to find it completely empty. Her face is a Heartwarming Moment just by itself.
"Elogium" is a slightly ridiculous episode, but worth it for Kes's speech to the Doctor, where she all but admits he's a Parental Substitute now that she doesn't have her own father. The Doctor, despite being out of his depth, awkwardly but sincerely tries to provide the guidance she so desperately wants.
Tuvok's description of his own role as a father to his children, and his extremely blunt correction when Neelix asserts a father would have nothing to teach a daughter.
The climactic scene of "Twisted," and probably the best part of the episode, is when the Negative Space Wedgie passing through the ship is about to overtake the holodeck where the crew members are trapped. Tuvok's solution is... nothing. They've tried everything, and now all they can do is let it consume them and see what happens. In the face of potential death, Tuvok and Chakotay take a moment to settle their differences and give respect where it's due:
Chakotay: You know, Tuvok, I may not get another chance to say this. Sometimes I find you arrogant and irritating, but you're a hell of an officer.
Tuvok: Thank you, sir. And since we are speaking candidly, may I say, sir, that I have not always been particularly partial to your methods either.
Chakotay: I suppose it must have been tough for you to accept my being elevated to first officer over you.
Tuvok: I have always respected Captain Janeway's decisions. However, I suppose that particular decision did put me in a position I am unaccustomed to. If that ever caused me to make things more difficult for you, I must apologize.
Chakotay and B'elanna then take their possible last moment to hold hands, while Tuvok goes to be by an unconscious Janeway's side, a True Companion to the end.
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.
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.
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.
Q: 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.
Also the episode presents us with an unambiguously good member of the Q Continuum in the form of Quinn. He ensured the Borg wouldn't assimilate the Federation by saving the life of Will Riker's ancestor, gave us a huge advance in science by helping Sir Isaac Newton, and helped Maury Ginsberg meet his future wife at Woodstock. And unlike the other Q, his lessons to humanity didn't come with loss of life or strings attached. A true cosmic good samaritan.
"Lifesigns", in which the Doctor first experiences love... with Danara Pel, 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.
Honestly, that whole episode. From the Doctor's fumbling around coming to grips with how he feels for her, to Kes being a hugeShipper on Deck, to their holodeck date together (set to old doo-wop music), to the Doctor's first kiss. Of course, it helps that Susan Diol and Robert Picardo have dynamite chemistry the whole episode.
Denara's first activation as a hologram is really touching. She looks in the mirror and sees her unblemished face for the first time in who knows how long (equally a surprise for the audience; a healthy Vidiian hadn't been seen till now). Her reaction is Tears of Joy.
When Neelix finds out Tom is leaving the ship in "Investigations," he shows up begging him to stay, then hugs him. Then, with his new program A Briefing With Neelix, he delivers this fond farewell for Tom that would serve equally well as a eulogy. Keep in mind that Neelix, for the longest time, thought that Tom was just a Lothario trying to steal Kes away from him. This could be considered the first real glimpse of the more approachable Neelix we'd see in later seasons.
Neelix: I'm proud to say that in spite of my narrow-mindedness, Thomas Eugene Paris became my friend. I'm going to miss him. No more laughs over a game of pool. No more sitting up into the wee hours swapping stories. No more complaints about my cooking. Goodbye, Tom. I think I speak for more of us than you might imagine when I say you're going to leave an empty space when you go. I hope you find what you're looking for.
Tuvok's interaction with the Drayan children in "Innocence". Although they are completely different species, Tuvok's paternal feelings are alive and well. At one point, he sings them a bedtime song, which he used to sing for his children. This is also very sad when you realize that he might not be able to do anything like that for his children again.
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.
Sad as hell, but Lon Suder's Heroic Sacrifice lets him redeem himself for his past crimes. Then there's Tuvok's words as he says his goodbye.
Tuvok: I offer you a Vulcan prayer, Mr. Suder. May your death bring you the peace you never found in life.
"Flashback" has a beautiful Platonic Life-Partners moment for Janeway and Tuvok. A Mind Meld is needed in order to help out Tuvok's sudden memory issues, and commonly, for Vulcans, this kind of therapy is done by a family member. Janeway immediately tells the Doctor that she's the closest thing to a family member Tuvok has on the ship, and Tuvok, from his bed in Sick Bay, wholeheartedly agrees. In fact, he confides that he prefers to meld with Janeway over any of the Vulcans on board Voyager. The sweetest Hand Wave ever.
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!
A small detail but, Janeway smiling whenever Rand gave Tuvok a friendly ribbing.
In "The Chute", Tom and Harry are locked up in an alien prison and being driven mad by implants put in the heads of prisoners. At one point, a prison mob tries to beat up Tom, who is gravely injured, but Harry stands against the entire mob, refusing to let Tom be hurt. Unfortunately, in a later scene, Harry attacks Tom after Tom, out of his mind from the implant and his injury, destroyed their only means of escape, and it's the latter incident that Harry fixates on after the rescue... until Tom sets him straight.
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.
"Future's End" when the Doctor steps outside, on 20th century Earth, for the first time. It's the debut of the mobile emitter, and the awe on the Doctor's face is just wonderful.
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.
Q: By the way, did I tell you how smart he is? I've already taught him how to knock small planets out of orbit.
Twofold one in "Worst Case Scenario." First, Tuvok had set aside the Insurrection Alpha training program, meant to train his security personnel for the event of the Maquis crew revolting and taking over the ship, when he realized that the crews were getting along better than he'd expected and believed that it might create the situation it was meant to prevent (logical or not, it's still heartwarming to realize how much a Vulcan cares about morale).
Then, when it IS discovered by the crew, rather than being something the fractures and divides them, there's a great deal of fascination and genuine enthusiasm for the idea of basically LARPing themselves in a situation that none of them believe will happen - after three years, the Voyager crew are a single crew, and the division of "Starfleet" and "Maquis" means nothing in practice anymore, and instead of a tactical training program, they're seeing it as almost a community endeavor and entertainment.
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. Chakotay responds by just being True Companions personified.
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.
In "The Gift", Kes' powers suddenly surge and she is forced to leave the ship before she inadvertently destroys it as she becomes an energy being. The episode's title comes from her last line: my gift to you. In gratitude to the ship's crew, she sends the ship about 10,000 light-years ahead, significantly reducing their journey. And just before the credits roll, Tuvok dresses in his formal Vulcan robes and lights a meditation candle in the window of his quarters as a tribute to her while the camera pans out into space. Also a hugeTear Jerker, if you're a big Kes fan (and many Voyager fans are).
The entire time, Beware the Superman crosses the mind of exactly nobody. Everyone treats Kes' new abilities with pure amazement and wonder. Even when her powers threaten to tear Voyager apart, there's never a hint of ill-will, just concern for her safety as much as the ship's. We've come a long way from the days of Gary Mitchell.
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. Also, say what you will about Neelix, but the offer was pretty touching in itself.
Neelix: You may use me to blow off steam. When you're angry, come see me. Call me names, insult me, question my parentage. I won't take it personally. And you won't need to keep things bottled up inside anymore.
Torres: That may be the nicest offer I've had in a long time. Thank you, Neelix. You're sweet, but I'm not sure I could do that to you.
Tuvok:(sitting down next to her) I will join you for a glass of wine.
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.
In addition, while the ship is deteriorating through the Year of Hell, Chakotay is kind enough to remember Janeway's birthday, even when it was the last thing on her mind. Too bad about the birthday present, though.
In the new timeline, the Krenim are much more friendly. Politely advising Janeway that "this area of space is under dispute" and suggests Voyager avoid it. Which she's more than happy to do.
Even the villain gets a happy ending. In the reset timeline he finally got what he'd been searching for the entire time — his home colony restored and his beloved wife returned to him. The final scene of the episode is him putting aside the temporal calculations that got him into this whole mess in the first place, and spending time with someone who loves him.
In "Mortal Coil," Neelix assembles a medicine bundle for a vision quest. Among the items is a flower from Kes's garden. Despite her having left the ship, he still cares for her.
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.
The Doctor: The warbirds are in retreat! EMH Mark 2: Doctor, we've done it! Two holograms, alone: Romulans on one side, Starfleet on the other. Alarms beeping everywhere. The Doctor: EMH Mark Two, newborn but filled with courage ... EMH Mark 2: EMH Mark One, armed with years of experience ... The Doctor: Together they emerged triumphant. EMH Mark 2: The end. (console beeps) Or not? (Two armed Starfleet officers beam aboard.) The Doctor: Welcome to the Prometheus, gentlemen. It's about time.
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.
B'Elanna deserves special mention. Despite being grief-stricken at the message that the Maquis had been wiped out in the Alpha Quadrant, she still makes a point of personally delivering the final letters to Harry (who she knows is increasingly desperate to hear from his parents) and Tom (conflicted over the message from his father).
Tuvok, though Neelix pesters him to immediately read the letter from his wife, intends to complete the work he's doing first. Neelix says that he inadvertently read the first few lines when checking to see who it was for, and reads them out to Tuvok, revealing that his eldest son has taken a mate and fathered a daughter, making Tuvok a newly minted grandfather. Neelix leaves, Tuvok resumes his work for a moment...then succumbs to the desire to read the rest of the letter. That's touching coming from a guy who's ostensibly emotionless.
"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 traveling for months through a soul-crushingly empty, starless void, one lonely star appears on the viewscreen. Then another. And another. Andthen...◊
B'Elanna, just before they initiate their plan to escape the void: See you on the other side.
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 production. The fact that by the end of the episode the loss of "One" is enough to cause a genuine tearjerker 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 anymore, they just show up and look helpless.
B'Elanna at the end of "Extreme Risk," eating her childhood favorite — banana pancakes. After one of the most harrowing episodes of the series, dealing with trauma, guilt and self-harm, the little smile she makes after one bite is very satisfying.
In "Once Upon a Time," when Tuvok and Samantha Wildman are stuck on the Delta Flyer 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, and she can trust that her daughter's remaining guardians will care for her.
Wildman: Who's going to look after Naomi?
Tuvok: You should not concern yourself with that now.
Wildman: How can you say that?
Tuvok: My youngest child has been without a father for four years, yet I am certain of her well-being, that I conveyed my values to her before leaving. And I have confidence in the integrity of those around her. You have been an exemplary mother to Naomi, and she is in the hands of people you trust. She will survive and prosper, no matter what becomes of us.
Wildman:[moved] Thanks, Tuvok.
Also in this episode: Samantha's daughter, Naomi, has been absolutely horrified to learn her mother might have died on their away mission, which makes it all the more satisfying when Samantha finally gets back on the ship to give her brave little girl a big hug.
Earlier, as Captain LaForge is pursuing the Delta Flyer trying to stop Chakotay and Kim from altering the timeline, he admits to Chakotay that, were their positions reversed, he'd be doing the same for his crew. But he must do his duty. Both men wish each other the best of luck in their mutually-opposed missions.
While "Course: Oblivion" is mostly a Tear Jerker, in a bitter way, it's sweet to see Biomemetic Neelix walking around amongst the dying crew, doing whatever he can to make them comfortable.
"In that book which is my memory, On the first page of the chapter that is the day when I first met you, Appear the words, 'Here begins a new life'."
"Gravity." Tom, Tuvok and the Doctor are stranded for two months on a Scavenger World, and no one else for company except for Noss, a woman who's been stranded and struggling to survive for years. Right from when Tuvok saves Noss from a gang of thugs, Noss develops strong feelings for Tuvok, and despite the circumstances, her advances are actually really cute. Especially when she tries to get to know him better while they make dinner.
Noss: Tell me about you there. Tuvok: I am the Chief Tactical Officer. Noss: What else? Tuvok: Can you be more specific? Noss: Your duties. Uh... where you sleep. What you eat. Music. Friends. Tuvok: Why is any of that relevant? Noss: Because it is you.
For obvious reasons, Tuvok cannot return those affections, and Noss doesn't take it too well. Yet, after Voyager rescues them, he shows a rare moment of compassion for Noss. Right before he beams Noss back to her home planet, Tuvok has a private moment with Noss, and gives her a brief Mind Meld, communicating silently his real fondness for Noss that he could never bring himself to express verbally.
Noss (looking happy and satisfied): I understand. Thank you.
At the beginning of "Bliss", Tom and Seven start teaching Naomi how to pilot the Delta Flyer. Later on, she's fallen asleep and Tom is carrying her back to her mom's quarters and it's adorable.
"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 "Survival Instinct", Seven admitting that she considers Naomi family.
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 fulfilment, with 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 medal she's just presented him. To which he responds:
Doctor: 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.
Phlox (no, not Dr. Phlox), the alien spy looking in on the Doctor's daydreams, decides to help him and Voyager because looking at the Doctor's fantasies allowed him to see that he could be something better.
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.
Also, the fact that Neelix initially tries to get Tuvok back to normal after he's shot. Neelix generally seems to feel that Tuvok doesn't have enough feeling in his life and tries to get a smile out of him, but he's not about to do it in a way that involves taking unfair advantage of his condition. Which is some pretty nice Character Development, when you think about it.
The better part of "One Small Step," especially Seven's speech. 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:
And then Tom gives the greatest smile. He's the history buff, and he understands.
Even people who aren't huge Voyager fans love the ending to "Pathfinder." 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. The look on Tom's face when he first hears his father's voice is especially great - he's silent the whole scene, but his face upon hearing his father is just "...Daddy?" Especially poignant because they had been estranged due to Tom being cashiered from Starfleet and convicted for his activities with the Maquis. 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.
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.
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: Hear, hear! To Mr. Barclay!
The scene near the end of "The Voyager Conspiracy" how Janeway convinces Seven to come back to Voyager.
In "Muse", Tuvok's clear concern for B'Elanna and Harry's fate. He is so worried that he goes ten days without sleep, relentlessly working to find them. (It ends in a Funny Moment when Tuvok falls asleep in the captain's chair, but it was the thought that counted!)
This is in fact contrasted with the alien actor performing the role of Tuvok, expressing his discomfort with the character's lack of expressed emotion - while they talk about how the audience will struggle with being unable to see the emotion under the mask, Tuvok displays just how an audience can see his emotions without being expressed.
Kelis closes out his play with a touching speech, wishing Voyager farewell:
"And Voyager will continue on her journey to the gleaming cities of Earth where peace reigns, and hatred has no home."
Harry finally turns up, two thirds of the way through the episode, after being presumed dead, and an overjoyed B'Elanna gives him a hug. And B'Elanna's not exactly a huggy person!
Episode "Life Line": Among the news Pathfinder delivers to Voyager is that Lewis Zimmerman, the creator of the Emergency Medical Holograms is dying of an incurable disease and the Doctor thinks that he could cure him with the medical information they have discovered in the Delta Quadrant. He is transported to Zimmerman, who at first wants absolutely nothing to do with the Doctor, seeing him as a reminder of all the failures of the EMH project that was supposed to be his crowning achievement. It takes plenty of convincing to even allow the Doctor to operate on him. Afterwards, Zimmerman does admit he is grateful that at least one of his holograms is doing the work he wanted and that how the Doctor has developed on his own is rather impressive. Which is all the Doctor wanted to hear from his creator.
Another heartwarming part in the episode is Zimmerman's assistant Haley, who is the first autonomous hologram he ever created. Zimmerman appreciates her to the level where he once canceled a lecture on Vulcan to fix her, and has arranged in his will that after his death Haley is to be kept online indefinitely.
Seven putting the Borg children "to bed" at the end of "Collective".
"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.
Seven of Nine gets a little one of her own. Since she joined the crew, she's always hated being called Annika. Then she gets the chance to talk to her aunt from Earth for the first time since before she was assimilated. Her aunt, delighted to see her again, calls her by that name, and Seven is notably silent.
In general, the crew defending the Doctor's rights as a sentient being is just a joy to watch, showing that he really did earn everyone's respect over the years with his Character Development. Janeway in particular makes an impassioned defense, demonstrating how far she's come since "Latent Image."
Particularly poignant when you consider that everyone on the ship — even the lower-ranking crewmembers we don't see interacting with the Doctor that often — must have agreed to sacrifice (or at least delay) their own chances to communicate with their loved ones on Earth so that the senior staff could defend the Doctor's rights as an individual in court; he might have started out as a simple back-up medical officer, but clearly everyone on Voyager agrees with Janeway's expressed sentiment that the Doctor deserves the same rights as the rest of the crew.
A small moment, but a moment nonetheless. When talking about places on Earth in "Imperfection", Seven brings a picture of Bloomington, Indiana (Janeway's hometown) up on the screen to show it to the captain. When the camera cuts to Janeway, we see her absolutely beaming at the picture.
From the same episode, we have Torres shielding Seven, at least for a while, from being found by the Doctor, telling her that she's escaped the Doctor herself once or twice. Seven asks her if she believes that her soul will go to Sto-Vo-Kor and she says she supposes it would depend on whether she dies an honorable death, but she does hope that there is something after death. Seven explains that the Borg have no concept of an afterlife, but the memories of each drone are retained in the collective consciousness after being deactivated, so in a way they survive so long as the Borg do. She, however, has been severed, so nothing would be left. Torres tells her that she's a little more memorable than she's giving herself credit for, that she's made an impact on every member of the crew. The fact that the whole thing comes across is completely sincere is both quite heartwarming and a real tribute to how far relations between the two characters have come, given that at first Torres could hardly stand to be in the same room with Seven without wanting to hit her.
In "Drive," Tom's declaration that the only kind of person that he wants to be is the kind that Torres is in love with.
The young Q Junior in "Q2" making friends with Icheb after he's turned into a human, including the way they call each other "Itchy" and "Q-ball". When Icheb's life is endangered because of Junior's mistakes, Junior is even willing to sacrifice his life for his only friend. And at the end of the episode, a reempowered Junior repays "Aunt Kathy" for helping him by filling her office with roses.
Tom and B'Elanna's talk in "Lineage" where B'Elanna admits that part of her still fears that she was responsible for her father leaving her and her mother when she was a child because he couldn't handle her Klingon heritage, only for Tom to assure her that he would never do that to her and their daughter and that he hopes all their other children are just like her, ridges and all.
The scene in "Homestead" when Tuvok dances for Neelix; after all this time we find that Tuvok really, honestly developed some serious respect for him. But that's just the tip of the iceberg - "Homestead" is an episode of heartwarming for Neelix. Some forty thousand light years from Talax and the rest of his entire species, Voyager discovers a colony of Talaxians struggling to establish a home. In helping to defend their colony, he finds himself torn between staying with them or going with Voyager. When they prepare to leave, Janeway, recognizing his conflict, makes a proposal — Voyager and Starfleet need an official ambassador to the Delta Quadrant, which, if he accepts, allows him to stay with the Talaxians but also stay in contact with his friends and family on Voyager, even as they continue their travel to Earth. Neelix, of course, accepts, and he gets a beautiful hero's sendoff, with the whole crew lining the corridor on his way to the transporter. After Growing the Beard in the last few seasons, Neelix deserved it.note On a meta-note, those are actually extras and members of the crew who were put into uniforms, and put on camera, just to make it extra special for Ethan Phillips. Jeri Ryan later admitted she was "blubbering" while shooting this episode.
At the end of "Endgame", where after seven years, Voyager finally gets home.
Janeway (stunned): ... We did it.
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:
Harry: 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.
Plus, there's Neelix's final scene of the series — having left the ship to join a Talaxian colony, he and Seven have arranged to have regular contact and play kadis-kot. During their game, he mentions to Seven that he's thinking of asking Dexa, a woman he'd grown close to in "Homestead," to marry him. Seven says that Dexa "would be wise to accept," said with open affection (by her standards) for Neelix.
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. Several scenes make it clear that Seven absolutely will go to bat for Naomi, protect and support her, in small things and big.
Especially apparent in season five episode "Bliss", during which Voyager is stuck inside a massive telepathic organism that has convinced the entire crew—except Seven and Naomi—that it's a wormhole that will take the ship directly to Earth. At one point, Seven picks up a frightened Naomi and carries her. Awwwwww.
The redemption of Tom Paris and B'Elanna Torres. Tom was dishonorably discharged from Starfleet, then captured soon after joining the Maquis and sentenced to prison, which pretty much breaks his relationship with his distant admiral father. When he arrives on Voyager, he is greeted coldly by several of the crew, and the Maquis don't like him any better — he just worked for them for the money, then helped Voyager track them down. B'Elanna is little better off, having dropped out of the Academy under circumstances that did a number on her confidence (she thought she couldn't make it in Starfleet, though as mentioned above, her teachers thought highly of her potential), still struggling with abandonment issues thanks to her father, and carrying a lot of anger. By the time Voyager gets back home, they are Starfleet officers in good standing, married, and raising a family. On top of that, Tom's repaired his relationship with his father.
In an interesting sense, the opening. It's a series of shots of Voyager flying through all kinds of scenic environments alone, with the soft but resolute and inspiring theme playing. This is a ship that's stuck on its own trying to get home, but that's OK. They crew have got quite the journey to go through, but also an amazing series of things to see and they're all in it together. Arguably, it's Star Trek's optimism, wonder, and camraderie at its purest.