TOS - Amok Time
TNG - Yesterday's Enterprise
DS9 - Trials and Tribble-ations
VOY - Year of Hell (1) and (2)
ENT - In a Mirror Darkly (1) and (2)
FILM (in my opinion, before the 2009 film) - First Contact
TOS - Balance of Terror
TNG - All Good Things 1 & 2 (they went out with a bang)
DS9 - Er, um, didn't really watch it enough to say...
VOY - ditto
ENT - um... ditto
Movies - Wrath of Khan / First Contact
TOS - I like the one where the lady has been in a terrible accident and had to have reconstructive surgery and her face is covered in bandages and the doctors take off the bandages and she's horrified at how ugly she is but then the camera cuts to her face and she's gorgeous and then the camera shows the doctors and nurses and they're horribly ugly and we're like WHOA MINDF*CK
TNG - My favorite is the one where they meet the other Battlestar but they almost get in a fight because Cdr. Adama doesn't want to follow Cain's crappy orders but eventually Cain gets killed and Adama gets promoted.
DS9 - Man I like the documentary they did on Nostradamus, that was pretty awesome, and how his prophecies weirdly coincided with Mayan predictions and I was like WHOA MAN DEEP.
VOY - I like the one with the green people.
ENT - Gotta be the one where the Martians try to take over the world and they start killing people and everyone's like AHHHH WE'RE GOING TO DIE AHHH but then the Martians die because they get all kinds of Earth diseases because they've never been exposed to Earth microorganisms before and I was like whew that was close.
FILM - The one with the Nazis and Brad Pitt.