(Mostly in order by seasons of each series)
"Star Trek"
- Seeming completely out of character, Spock attacks the Salt vampire, yelling
"If she were Nancy, could she take THIS?" as he throttles her in
"The Man Trap" 
- Riley:
"And now crew, I will render 'Kathleen' ONE...MORE...TIME! time"
Kirk:
"Please...not again."
(
"The Naked Time")
- The Romulan Commander's death in
"Balance of Terror"
- Spock hanging from a tree and laughing in
"This Side of Paradise"
- Khan and Marla kiss for the first time in
"Space Seed" (mostly because of that great shot of her hands going up his back)
- Kirk tells Spock he's in love with Edith Keeler and Spock says she must die in
"The City on the Edge of Forever"
- Spock's embarassingly elated
"Jim!" in
"Amok Time"
- When a smiling Trelane gets smacked without even flinching in
"The Squire of Gothos"
- DeForest Kelly and Julie Newmar slap each other in
"Friday's Child"
- Spock's mother slaps him in
"Journey to Babel" (a lot of great moments in
"Star Trek" revolve around people hitting each other
)
- Mirror Kirk yells about how he can get Spock power in
"Mirror, Mirror"
- The tribbles fall on Captain Kirk in
"The Trouble with Tribbles"
Star Trek: The Next Generation
- Lore challenges Worf in
"Datalore"
- Riker gets punched in the face at the end of
"A Matter of Honor"
- Riker switches off Data
- Guinan makes Picard realize that they're talking about slavery
in
"The Measure of a Man"
- Both Picards say
"undahstood!" at the same time in
"Time Squared"
- When Picard sees what the Borg ship is doing, says
"let's get the hell out of here!" and then admits that he needs Q in
"Q Who"
- Data says
"I busted him up" and can't resist a rather out-of-character smile in
"Peak Performance"
- Picard yells at Q to get rid of his mariachi band in
"Deja Q"
- Lal kisses Riker and Data asks what his intentions are in
"The Offspring"
"Not good enough, dammit! Not good enough!" - Picard yells at Guinan in
"Yesterday's Enterprise"
"No help for the Klingon" in
"Cause and Effect"
- Guinan's pre-battle conversation with Picard
- Picard as Locutus calling Riker "Number One"
-
"They're carving us up like a roast"
- Riker ordering Worf to fire
in
"The Best of Both Worlds"
- Picard confesses to his brother how he felt about being assimilated in
"Family"
- Picard and Vash kiss after Picard saves her in
"Qpid"
- Ardra turns into Troi to try to seduce Picard in
"Devil's Due"
- Riker's "promise" at the end of
"First Contact"
- Picard freaks out because he thinks the elevator is going to crush him in
"Night Terrors"
- Data pops out from behind the bar and offers to get everyone a drink in
"Conundrum"
- Scotty and Picard toast their ships in
"Relics"
- Moriarty appears to step off the holodeck in
"Ship in a Bottle"
- Spider-Barclay pops up in engineering in
"Genesis"
- Picard joins the Poker game in
"All Good Things..."
Star Trek: Deep Space Nine
- Sisko bellows that he'll kill Kira in
"Dramatis Personae"
- O'Brien finds out what's been going at the end of
"Whispers"
- Quark hits on Keiko in
"Fascination"
- Sisko becomes Joran in
"Facets"
- Garak is disgusted as Bashir seduces the female scientist in
"Our Man Bashir"
- Rom cries out for "Moogie" in
"Little Green Men"
- Michael Eddington compares Starfleet to the Borg in
"For The Uniform"
- Weyoun swears obedience to Odo
- Jadzia answers a Jem'Hadar solider's question about her age
in
"To The Death"
- Jadzia Dax shrugs at Captain Kirk in
"Trials and Tribble-ations"
- Bashir cuddles up with his bear
- Sisko checks out the baseball card and gives Jake a hug
in
"In the Cards"
- Dukat examines Sisko's baseball and tells Weyoun what it being left behind means in
"Call to Arms"
- Jadzia and Worf are married in
"You Are Cordially Invited..."
- The accidental death in
"The Magnificent Ferengi"
- Sisko storms into Garak's shop and punches him in
"In the Pale Moonlight"
- The kiss at the end of
"His Way"
- Ezri introduces herself to Sisko in
"Shadows and Symbols"
- Everybody laughs at the Vulcan in
"Take Me Out to the Holosuite"
It's fun to reflect on my favourite moments of
"Star Trek: Deep Space Nine" as I'm only three episodes away from finishing watching the series for the first time. I imagine I may have some more favourite moments in the two part series finale.
