During Voyager's battle with the Kazon in "Basics Pt. 1", the crew try to fool the attacking ships with some holographic ships. Unfortunately, when they initiate the program, the Doc somehow gets stuck floating outside the ship as the battle ensues and cries "Man overboard!" What's the first thing he says once B'Elanna transfers him back to sickbay?
B'Elanna: Doctor, are you there? Are you all right?
Doctor: I told you, we should have run one last systems check.
In "Basics Pt. 2", most of the crew has been dumped onto a Stone Age planet. Chakotay says this as they're trying to start a fire:
"Sorry that you're stuck with the one Indian in the galaxy that can't make fire by rubbing two sticks together."
Tuvok: Asking female officers for their clothing could lead to misunderstandings.
''This is followed by a scene of Janeway on the bridge wearing Rand's obviously ill-fitting uniform.
Fridge Logic: It's a good thing memory is solipsistic, or Rand might have had to explain how she wound up stuffed in a closet in her underwear.
The episode "False Profits" is full of laughs (thanks mostly to the Ferengi Arridor and Kol). One moment that really stands out would be near the end of the episode. When it looks like the two Ferengi and Neelix (who was disguised as a Ferengi at the time in order to try and get the two to leave the planet) are about to be burned at the stake as the jubiliant and enthusiastic (but horribly misguided) locals attempt to send them back up to their home in the sky "on wings of flame" in the words of the ancient prophecies they're following.
Arridor: What is it now?!
Kol: We had seven years of pure profit.
Arridor: (smiles) We did didn't we?
Neelix: (Neelix gives them both a look of pure confusion and disgust)
"Message in a Bottle". Take any pick of EMH Mk II and the Doctor's interaction, especially the one when they talk about sex, and Mk II's lament.
Don't forget this one.
Computer: specify attack pattern. Mark I: Attack pattern... (thinks for a sec)... Alpha? Computer: State target. Both EMH's: ROMULANS!
Yep, and these ones:
Mark I: Stop breathing down my neck! Mark II: My breathing is merely a simulation. Mark I: So's my neck, stop it anyway!
Mark I: You hit the wrong ship! Mark II: It wasn't my fault! Mark I: Well whose fault was it then, the torpedos'? You're supposed to tell it what to do!
Mark II: What are they doing?! Mark I: Firing on us! Mark II: They must think there are Romulans on board! Mark I: THEY'RE RIGHT!!
The same episode also gave us Seven knocking a belligerent alien unconscious with an electrical shock. She explains:
Seven: He was not responding to diplomacy.
"Get the cheese to sickbay!" and "There's coffee in that nebula!"
From the cheese episode, the Doctor eventually gets the idea to deal with the infection like a human body would: roast it with a fever. After dialing up the heat on the ship to cleanse the gel-packs, he proudly announces success. Then the camera pans over to Kes, who is dripping with sweat while the holo-Doc is no worse for wear.
When Seven is drunk in "Timeless", and pretty much every moment when The Doc is stuck in her body in "Body and Soul".
In "Infinite Regression," Jeri Ryan's Ferengi impression.
In "Revulsion", when Seven was trying to seduce poor Harry in her usual blunt way, forcing him to confront his inarticulate crush on her. (Poor, dumb Harry.)
Kim: I don't know what you're talking about.
Seven: Obviously you've suggested a visit to the holodeck in the hopes of creating a romantic mood. Are you in love with me, Ensign?
Kim: Well, no.
Seven: Then you wish to copulate?
Kim: No! I mean, I, I don't know what I mean.
Seven: All of these elaborate rituals of deception. I didn't realise becoming human again would be such a challenge. Sexuality is particularly complex. As Borg we had no need for seduction, no time for single cell fertilization. We saw a species we wanted and we assimilated it. Nevertheless, I am willing to explore my humanity. Take off your clothes.
Kim: Er, Seven.
Seven: Don't be alarmed. I won't hurt you.
EMH to Neelix when they're being dragged into a battle by Klingons: "You heard the man, run along. I'll reattach any severed limbs, just don't misplace them." Then the Doc gets dragged along with them.
Holo Klingon: Qapla!
Doc: (waving a knife) Tally-ho.
Many moments in "Tinker Tenor Doctor Spy", but a special mention goes to the Doctor's aria in the teaser and the briefing room scene.
Also in that episode, some of the crew, including Seven, enter the Doctor's daydream to discover that he's imagining doing a nude portrait of Seven. Janeway just looks at the picture and finally observes that "he's very good at the hands." (Likely a Call Back joke to the "hands of a surgeon" joke on DS9)
The computer in the Doctor's daydreams (voiced by Majel Barret, as usual) gets in some good lines, too:
Warning: Warp core breach a lot sooner than you think.
Warning: Last chance to be a hero, Doctor. Get going!
"Bride of Chaotica". Watching the crew play around in a sci-fi serial from the 1930's is funny enough, but there are two lines in that episode that take the cake. When Tom Paris is explaining to the senior staff how to stop Chaotica, he says, completely serious, "The Destructo-Beam on my rocket ship can disable the Death Ray, but only if someone gets inside the Fortress of Doom and can shut down the Lightning Shield." When Janeway starts questioning the ridiculousness of this,
Captain: Let me get this straight, transdimensional aliens have mistaken your Captain Proton simulation for reality?
Paris: Yes ma'am.
Captain: And now an armed conflict has broken out between these aliens and Chaotica's holographic army?
Paris: (completely deadpan) Yes ma'am. His army of evil.
When Tom recommends that someone take on the role of Queen Arachnia, Janeway sarcastically asks who he had in mind, at which point she and all of the other officers in the room turn to look at Seven. A couple moments pass, and then Janeway turns back around to see that Tom is looking straight at her.
"See you at the Fortress of Doom! And remember. You're the Queen!"
Any and all instances of the magnificent Large Ham that is Doctor Chaotica.
FoooooOOOOOOOOOOOLLLLLLLLL!!!! You will pay for your inCOMpetence!!
Later on, Janeway gets into the spirit of the thing and really hams it up, delightfully yelling, "HA! You're no match for Arachnia!"
In "Critical Care" the crew have to track down the Doctor's kidnapper. They ask a lady who dated (sort of) the kidnapper and she accuses Janeway of wanting the man for herself. Instead of trying to convince the woman of the truth, she grabs Tuvok's hand and says, "I already have a man." Tuvok looks as uncomfortable as a Vulcan can be. AND IT IS HILARIOUS.
In "Q2", Janeway tells Q he needs to spend more time with his son to rein in said son and Q thinks this is a great idea. He kisses Janeway full on the mouth and disappears. The expression of shock and disbelief on her face has to be seen to be believed. Here, have a look.◊
Q has to discipline his son for bringing Voyager into contact with three Borg cubes.
In the same episode, Q Jr. (lower-case q?) turns engineering into a rave party.
"Projections" has several, especially:
Doctor: Computer, delete Paris.
After B'Elanna is infected with Vorik's Pon Farr, Paris is informed that he needs to have sex with her to keep her from going insane and dying (and at this point they're not yet a couple) and all but ordered to do so. The expression on his face (kind of a combination between "Man, all that holding her offwas for nothing!" and "Well,okaythen!") is priceless.
And their encounter at the end:
Paris: You're afraid that your big, scary Klingon side might have been showing. Well, I saw it up close and you know, it wasn't so terrible. In fact, I wouldn't mind seeing it again someday. B'Elanna:Careful what you wish for, Lieutenant.
When Seska is revealed to have been a Cardassian spy, Chakotay laments to Tuvok (who had also been a spy on his ship, for the Federation), "Was anyone on that ship working for me?"
The bridge crew muting the EMH in "The Cloud".
Torres discovering Seven has been keeping notes on her and Paris' love life.
Torres: How the hell do you know when we're having "intimate relations"?!
Seven: (deadpan) There is no one on Deck 9, Section 12 who doesn't know when you are having intimate relations.
The future Paris on the Doctor finally choosing a name:
Paris: Joe? It took you 33 years to come up with Joe?
Tom Paris rewrites the Doctor's holonovel in "Author, Author".
"You are about to embark upon a remarkable journey. You will take on the role of a medical assistant aboard the starship Voyeur. Your job will be to assist the Chief Medical Officer and learn to tolerate his overbearing behaviour and obnoxious bedside manner. Remember, patience is a virtue!"
Near the beginning of the "Future's End" two parter Janeway and Chakotay discuss what their ancient relatives were up to during the time period. During the conversation, Chakotay makes a comment that simply can't be approved under Starfleet regulations towards a ship's captain.
Janeway: (a random woman on skates bumps into the pair and apologies before she skates away) For all I know she might be my great-great-great-great grandmother.
Chakotay: (smiles mischievously) She does have your legs.
Janeway's reference to Spock's famous "Bone knives and bear skins" line.
Tom has the pleasure of using the last line of the two parter to deliver a 20th century insult (which he picked up from Rain) to Tuvok.
Tom: (totally deadpan) You know what Tuvok, you're a real freakasaurus.
Henry Sterling's last words:
To clarify, this is the man who captured a time traveling ship after it fell to Earth in the 1970's, and has been a real Jerkass for the two part series. Eventually, after some on-the-fly repairs to the torpedo tubes, Voyager just barely manages to fire off a single torpedo at him as he is attempting to travel to the future—which is quite sufficient to obliterate him, however.
Decidedly the strangest sentence any Vulcan has ever spoken:
If you can get past the Nightmare Fuel that is two Borg cubes getting one-shotKO'ed by Species 8472 at the start of 'Scorpion,' the fact that they don't even get to their Catch Phrase of "Resistance is futile" (thus showing resistance is anything but) can be pretty humorous, and, based on that situation, you really need all the laughs you can get.
Any time Seven is in a social situation, and effectively has to order people to enjoy themselves.
In "Death Wish," a Q wants the right to die, and our old friend Q shows up, pushing them into a trial for his right to make that choice. Q calls forth character witnesses about the importance of this one Q to show that he should not end his existence, Isaac Newton, Maury Ginsberg, and Commander William Riker. The last knows and understands what happening. When Janeway tries to explain to the others...
Janeway: Consider for a moment that it might be possible to travel forward in time, say to the twenty-fourth century, onto a starship seventy thousand light years from Earth...
(blank looks from Newton and Ginsberg)
Janeway:(beat) You're having a very strange dream...
Dr Zimmerman is griping about how the EMH keeps trying to diagnose his illness, while receiving a soothing massage from a holographic Elloran female, who then covertly takes out a tricorder and starts to scan him.
Doctor: (smiles sheepishly as he returns to normal)
The Doctor and Zimmerman are both so abrasive that they drive the normally calm and understanding Deanna Troi to snap. "You're both jerks!"
In the episode "Nightingale", Icheb, inexperienced at relationships, especially romantic ones, thinks that B'Elanna might be expressing interest in him, despite being married. In perhaps the worst bit of reasoning possible, he asks the Doctor for advice on how to determine if someone is interested in someone else romantically. The Doctor gives very little useful information, and cites some biological symptoms of sexual attraction. Later, when working with B'Elanna in the tight confines of the Jeffries Tube, she uses Icheb's shoulder to lean on as she reaches up to access a system. He whips out his tricorder (not a euphemism) and scans her. The results (which presumably match the Doctor's suggested symptoms) cause his eyes to widen comically and he gets an almost terrified look on his face. Later Paris makes a friendly offer that Icheb join him in his race car program on the holodeck, which Icheb misinterprets as a human variation of a Klingon's mate challenging a romantic rival. Icheb quickly goes to "break up" with a confused B'Elanna.
In the otherwise creepy episode "Scientific Method" we have:
Tom and B'Elanna passionately making out at a semi-secluded engineering workstation. B'Elanna says she feels like she's being watched, Tom says she's paranoid, and back in the teaser this was because the alien scientists were monitoring them. This time it's because Tuvok has arrived.
After Chakotay is prematurely aged and Neelix is turned into a Myleean (dialated pupils, fused spinal column) they sit on a biobed and try to one-up each other with complaints like a pair of old men.