*“Captain, is there something wrong with your chair?”
But it was based on the submarine movie “The Enemy Below.”
My favorite Kirk line was also from The Doomsday Machine, when they decoy the killer away from the Enterprise. “Great, now it’s following us. Or I think it’s great - Scotty, get us out of here!”
Best Kirk line:
“I don’t say sabotage, I say saboTAHGE”
Another baseball one of Sisco’s is when he left his favorite baseball behind in his office when the Federation was forced to abandon the station.
And the Cardy stating- [paraphrase] “it means he intends to come back”
On the special edition of WoK Meyers talked abou t this line and how it took about 40 takes. Shatner kept telegraphing the punch and Meyers just had to wear him down to do it that way.
A slightly different type of “captain’s moment”, but…
In Wink of an Eye, Kirk and Deela in a clinch, fade to commercial…
…fade back to Deela brushing her hair, and Kirk zipping up his boots. For 1967, it was about as explicit as could be!
Heh, heh, heh. You’re too kind. Basically Meyer says that the only way to get a decent performance out of Shatner is to keep doing takes until Shatner gets bored, then you get the take worth keeping! 
This is also known as the worst decision ever by a Captain. leave the two most annoying characters ever dead next time, janeway!
Picard is trying to reason with the Sheliac, who are very letter-of-the-law types, and do not wish to talk with him. A loophole is found*. Picard requests 3rd party arbitration…with a species currently in hibernation for 6 months. Turns off the comm.
The Sheliac are hailing like mad. Picard says “not yet” and walks over and checks the dedication plaque for dust! Only then does he answer thier hail.
Priceless
How about Darmok? lots of good Picard moments there.
Brian
*by Troi I think. Yes, she does something useful!
Kirk to Scott, after the brawl with the Klingons in The Trouble with Tribbles.