"Balance of Terror"
(To Kirk) "In this galaxy, there's a mathematical probability of three million Earth-type planets. And in all of that, three million million galaxies like this. And in all of that, and perhaps more, only each and every one of us. Don't destroy the one named Kirk."

"The Devil in the Dark"
(When asked to treat the Horta) "I'm a doctor, not a bricklayer"

(After treating the Horta and has his hands full of concrete used to treat the Horta's wounds) "By golly Jim, I'm beginning to think I can cure a rainy day!"

"Amok Time"
(Last line) "In a pig's eye!"

"Friday's Child"
"I'm a doctor, not an escalator!" (okay, I like all of the "I'm a doctor, not a..." lines ^_-)

McCoy to Eleen's newborn baby: "Oochy woochy coochy coo. Oochy woochy coochy coo."
Spock: "Oochy woochy coochy coo, Captain?" Kawaii! (Japanese for "cute") ^_^

McCoy, telling the name of Eleen's baby and future high teer: "Leonard James Akaar."
Spock: "The child was named Leonard James Akaar?"
McCoy to Kirk: "Has a ring to it, don't you think, James?"
Kirk to McCoy: "It's a name destined to go down in history, Leonard. You think so, Spock?"
Spock: "I think you're both going to be insufferably pleased with yourselves for at least a month ...sir."

"Journey to Babel"
"Well, whadya know. I finally got the last word." The grin on his face is priceless ^_^

Star Trek II: The Wrath of Khan
McCoy tells Kirk he should get back to his ship before he grows old.

"According to myth, the Earth was created in six days. Now watch out! Here comes Genesis. We'll do it for you in six minutes!" Also, his arguing with Spock about the "right" hands for the Genesis project (seen in the network version and the DVD director's editon).

(featured in the network version and the DVD director's edition) After Scotty leaves sickbay distraught over his nephew Peter Preston's death, Bones laments how doctors lose patients sometimes. Then he asks Kirk how Khan managed to know about the Genesis project. Kirk is unsure how that was done but knows he and his crew must keep Khan's hands away from Genesis. While McCoy commends Kirk for outwitting Khan, Kirk said he managed to do so because he himself knew more about ships than Khan.

On Spock's death: "He's really not dead, as long as we remember him." I had as much tears in my eyes as Kirk and Spock's final goodbye (my other favorite moment) ;_;

Star Trek III: The Search for Spock
(Kirk retriving McCoy from Starfleet detention)
Kirk, giving McCoy the Vulcan salute: "How many fingers am I holding up?"
McCoy: "That's not very damn funny!" (It was to me ^_^)
Kirk: "Your sense of humor has returned."
McCoy: "The hell it has!"
Kirk gives an antedote to Bones for the effects of a Vulcan mind meld, courtesy of Spock: "You're suffering from a Vulcan mind meld, doctor."
McCoy, horrified: "That green blooded son of a b----! It's his revenge for those arguments he lost!"

(After rescuing Spock from the now-destroyed Genesis planet, McCoy is talking to an unconscious Spock)
"Spock! For God's sakes, talk to me. You stuck this damn thing in my head, remember? Remember? Now tell me what to do with it. Help me! [pause] Well, I'm gonna tell you something I never thought I'd hear myself say. But it seems that I've...missed you.... I don't know if I could stand...to lose you again." Even though Spock and McCoy had argued with one another, they actually cared for each other.

Star Trek IV: The Voyage Home
(McCoy asks Spock what death was like, only to get no satisfactory answers)
McCoy: "Do I have to die to discuss your views on death?!"

(Kirk and crew are observing the locals of 20th century San Francisco) "It's a miracle these people made it out of the twentieth century!" Not only is this line funny but it's also ironic, in that DeForest Kelley died in 1999, or to put it another way, Kelley didn't make it out of the twentieth century.

(Trying to get into the operating room to rescue Chekov, McCoy and Kirk have Dr. Gillian Taylor posing as a patient and two security guards block their way)
McCoy:"This woman has acute post-prandial upper abdominal distension!"
(The guards let them in)
Kirk to McCoy: "What did you say she's got?"
McCoy: "Cramps."

Star Trek VI: The Undiscovered Country
(Kirk kissed by Martia and McCoy "wakes" up after she leaves) "What IS it with you, anyway?"

Spock: "Doctor, would you care to assist me in an operation on a photon torpedo?"
McCoy: "Fascinating!"

General Chang via the ship's intercom: "I'm as constant as the northern star"
McCoy: "I'd give real money if he'd shut up!"

(The photon torpedo operation is complete)
Kirk via intercom: "Where's that damn torpedo?!"
McCoy: "She's ready, Jim! Lock and load!"

Kirk: "Once again, we saved civilization as we know it."
Mccoy: "And the good news is they're not going to prosecute!"

"Encounter at Farpoint", Star Trek: The Next Generation

McCoy: "Well, it's a new ship [the Enterprise-D] but she's got the right name. Now, you remember that, you hear?"
Data: "I will, sir."
McCoy: "You treat her like a lady, and she'll always bring you home."