Star Trek: Voyager/Funny

"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.
Doctor: Attack pattern... <thinks for a sec>... Alpha?
Computer: State your target.
Both EMH's: ROMULANS!

- Yep, and these ones:

Doctor: Stop breathing down my neck!
Mark II: My breathing is merely a simulation.
Doctor: 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 I: They're shooting at 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 responded simply:

Seven: He was not responding to diplomacy.

"Get the cheese to sickbay!" and "There's coffee in that nebula!"
When Seven was drunk in "Timeless", and pretty much every moment when The Doc was stuck in her body in "Body and Soul".
- Also from "Body and Soul": The Doctor-as-Seven discovers the joys of cheesecake.
- Also shows that Jeri Ryan is not just Ms. Fanservice, as she nails Robert Picardo's character.
In "Revulsion", when Seven was trying to seduce poor Harry in her usual blunt way, forcing him to confront his inarticulate crush on her. "Are you in love with me, Ensign?" "No." "Then you wish to copulate?" "NO!" "Then what do you want?" "I... I don't know!!"
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!
Neelix: ...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.
- "Tu-vok, I un-der-stand/You are a Vul-can man..." Also Crowning Music of Awesome.
- 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."
- 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: "Yes ma'am. [the slightest of pauses and completely deadpan] 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.
- Later on, Janeway gets into the spirit of the thing and really hams it up, delightfully yelling, "HA! You're no match for Arachnia!"
- "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!!

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.
"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 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 off was for nothing!" and "Well, okay then!") is priceless.
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 had been keeping notes on her and Paris's sex 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!"

Tom "rescuing" Harry from being "tortured" in a Captain Proton hologram. Really, he's not complaining about the mind probe.
Henry Sterling's last words:

Uh-oh!

- 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, Voyager just fires a torpedo at him as he is attempting to travel to the future.
Decidedly the strangest sentence any Vulcan has ever spoken:

Tuvok: It appears we have lost our sex appeal, Captain.

For the 30th-Anniversary special that aired on UPN, they put together (amongst other things) a mock audition for Voyager, featuring Kate Mulgrew... and the cast of Frasier (minus Kelsey Grammer). Out of Character moments, Deadpan Snarkery from Janeway, Lampshade Hangings and general silliness galore.
It was probably meant as a dramatic moment, but the scene where Tuvok choked Neelix to death, breaking his neck for good measure, left many viewers either cheering or laughing. Then it turned out that it was just a holodeck simulation.
Tom tries to get Seven involved in his Captain Proton simulation, the one mentioned above. He opts to give her the role of Constance Goodheart, Captain Proton's secretary. When faced with Satan's Robot, the scripted response from Constance is to scream. A lot. Seven marches up to it and rips out its wiring, shutting it down.

Satan's Robot: Citizen of earth. Surrender, do not resist.
Seven: I am Borg! (Seven nonchalantly rips out his wiring)
Satan's Robot: Surrender... (the robot shuts down)
Seven: The robot is disabled, may I leave?
Tom: Come on Seven, the galaxy's at stake.

Several moments from "Before and After" such as Doc's inability to choose and keep a name (Dr. Van Gogh in one time period, Dr. Mozart in another). Then we get these hilarious lines:

Harry: "So how does it feel to be a grandfather?"
Tom: "A lot better than it does to have you for a son-in-law."