I got a laugh out of Cochran’s “you’re on some sort of a Star Trek.” 
Neelix: “I will not rest until I get you to smile.”
Tuvok: “Then you will not rest.”
WORF (having listened with increasingly stony face as DATA recites an ever-lengthening list of instructions): I will feed him.
Nitpick:
It went
Kirk: “What happened to your crew?”
Decker: “I had to beam them down! I stayed here on the ship. Captain…last man…that’s what you’re supposed to do isn’t it!?”
Kirk: “Where are they now?”
Decker (after a pause where his face shakes from all the taut muscles): “On the third planet.”
Kirk: “Matt…there is no third planet.”
Decker: “DON’T YOU THINK I KNOW THAT!? There was, but NOT ANYMORE!”
William Windom rules.
Yeah, but what’s he doing in a “funniest star trek” thread? 
“The Doomsday Machine” is high drama for TOS!
Although admittedly its sometimes debatable whether its Windom or the Doomsday Machine which munches more of the scenery in the episode 
I think it was "never tell the same lie twice.
Which reminds me of a good Q line : “Oh please, don’t tell me the story of the boy who cried Worf.”
Counseller Troi about Barclay : “Let’s see, he just had a disease named after him and turned into a spider. I’ll clear my schedule.”
From STIV:
7th Heaven Mom: You’re from outer space?
Kirk: No, I’m from Iowa. I just work in outer space.
As much as I dislike Troi, I have to admit that this is a great line.
I still have to go with the falling-tribble scenes (both versions), though. This is one of the few cases where Shatner’s…excessive…pauses actually work.
Typo… honest!
GENESIS??? Genesis planet forbidden is!.
Spock: Surely you must have realized what would happen if you removed the tribbles from their natural, predator filled environment and introduced them into an environment where their natural reproductive proclivities would have no restraining factors.
Cyrano Jones: Ah, but of course…Er…what did you say?
He does indeed. I especially like in that ep how we get to hear his earlier taped logs, where he sounds competent, decisive, and composed, before he was overwhelmed by the disaster and lost his crew.
Alien: To your planet, welcome.
McCoy: I think that’s my line, stranger.
Alien: Oh, forgive. I here am new. But you are known, being McCoy from Enterprise.
McCoy: You have me at a disadvantage, sir.
Alien: Oh, I name not important. You seek I. Message received. Available ship stands by.
McCoy: How much and how soon?
Alien: How soon is now. How much is, where?
McCoy: Somewhere in the Mutara sector.
Alien: Oh, Mutara restricted! Take permits many; money more.
McCoy: There aren’t gonna be any damned permits! How can you get a permit to do a damned illegal thing? Look, price you name, money I got.
Alien: Place you name, money I name, otherwise bargain, no.
McCoy: Alright, damn it! It’s Genesis! The name of the place we’re going is GENESIS!
Alien: Genesis?
McCoy: Yes, Genesis! How can you be deaf with ears like that?
Alien: Genesis allowed is not! Is planet forbidden!
I love that speech.
Q: You’re so stolid. You weren’t like that before the beard.
and lastly:
Holo-Troi: “I am the goddess of empathy…”
Troi angry “Computer, discontinue program!”
Riker: “Computer, belay that order.”
What’s even funnier is his and her reaction when they run into the short Holo-Riker. Suddenly he fails to see the humor . . .
[Geek Mode]
Actually, I’m pretty sure you have the sequence reversed. Troi & Riker meet the short holo-Riker first; Riker begins to discontinue the whole thing, but Troi stops him, fearing (reasonably) the effects on reg of doing so suddenly. ("And after all,’ she points out, “you ARE very tall.”) A moment later they meet the bare-midriffed goddess of empathy, and troi is irritated enough to begin to delete it; riker stops her, feeling turnabout to be fair play.
[/geek mode]
Put me down for “I am NOT a merry man!”. I thought I would die laughing when Dorn delivered that line.
< shrugs > It’s possible; it’s funny either way.
Another one is the scene from Voyager where Ensign Kim hallucinates/dreams that 7 of 9 is coming on to him; she grabs hims, says “Resistance is futile” and kisses him.
Then theres a scene from The Search for Spock where the Katra-ridden Dr McCoy is confronted by this big Security guy. He reaches up and does the Vulcan neck pinch thing - or rather, tries too. Instead, he fumbles all over the guys neck while he gives McCoy this “What the HELL are you doing ?!” look.
My favorite “funny” Worf moment isn’t even played for laughs.
It’s the subplot in “The Icarus Factor” in which Worf walks around pissed all episode because he can’t complete the 10th Anniversary of his Age of Ascension Ritual. Galactic buttinskys Geordi, Data and Wesley Crusher recreate the ritual on the holodeck without realizing once the whole damn time they were programming it that its a gauntlet Worf has to walk through just to see how much pain he can endure.
As Worf takes each step forward he’s zapped repeatedly by holo-generated Kilogons holding electrified painsticks. By the end of the gauntlet he’s barely conscious and not quite walking upright. He finally makes it through and collapses to the floor. Before passing out he takes the time to growl to his horrified friends, “Thank you!”
Hee.
To briefly hijack, there’s a similarly funny line from the Trek novel Q-In-Law (highly recommended!):
Q: (addressing a crowd of visitors to the Enterprise) “You have to forgive Worf; he’s just discovered opposable thumbs and is feeling overconfident.”
Actually, I think the line is, “Captain, I must protest. I am not a merry man!”
That plus his costume is just hysterical.
Then there’s Barclay’s holosuite fantasy program, and Troi going on about how they must let it run to get an insight into his personality, until they stumble across the Goddess of Empathy. I think they heard her gasp of horror on the bridge.