Star Trek: The Motion Picture/Funny

• After Spock compares V'Ger to a child, McCoy replies "This child is about to kill all life on Earth. Now, what do you suggest we do, spank it?"
• McCoy again, after Spock rejoins the crew:

Spock: On Vulcan, I began sensing a consciousness more powerful than I have ever encountered -- thought patterns of exactingly perfect order. I believe they emanate from the intruder. I believe it may hold my answers.
McCoy: Well, isn't it lucky for you that we're heading your way? [does hitchhiking gesture]
Kirk: Bones!

• McCoy again:

Kirk: Well, for a man who swore he'd never return to Starfleet--
Bones: Just a moment, Captain, sir. I'll explain what happened. Your revered Admiral Nogura invoked a little-known, seldom-used reserve activation clause. In simpler language, Captain, they drafted me!

• Outtake first seen in the ABC-TV version:

After the transporter is fixed, an arriving crewman says "Someone wanted to first see 'how it scrambled OUR molecules'".
Kirk to Transporter Chief Rand: That has a familiar ring to it....

• • Given that this happened only a few scenes after Sonak's demise in that very same transporter, it's amazing that Kirk or the audience can find that funny.
    • A prime example of Gallows Humor.
• Not intentionally funny, but Bones appearing on the ship in a funky 70s robe-like uniform, full beard and "the eye piece of the Staff of Ra" around his neck definitely elicits a laugh.