Okay, I can't resist chiming in on this thread ...

[Full disclosure just in case ... a couple of "spoilers" ahead...]

Original Series

Favorites:

"The City on the Edge of Forever" - it's not cited as the best episode over and over for no reason; still terrific today, with everything from humor to heartbreak, and innumerable wonderful moments.

"A Piece of the Action" - my favorite lighthearted episode, though I also love "I, Mudd."

"This Side of Paradise" - has the best "last line" of any Star Trek episode.

"Who Mourns for Adonais?" - a premise that could have gone disastrously wrong turned into a great episode by Michael Forrest's excellent performance and -- like "This Side of Paradise" -- a grabber of a last line.

Least Favorites:

To the aforementioned "The Omega Glory" and "Spock's Brain," I would add "Let That Be Your Last Battlefield" and "The Gamesters of Triskelion."

The Next Generation

Favorites:

"The Inner Light" - quite possibly the best Star Trek episode ... ever.

"Yesterday's Enterprise" - riveting story with an incredibly dark tone, and also has the added advantage of letting Tasha Yar die a much more meaningful death than she experienced from the dreaded killer oil slick in "Skin of Evil."

"Best of Both Worlds" - the best season-ending cliffhanger ever: "Mr. Worf ...[wait]...[wait]... Fire!" [cut to black]

"Q Who" - I like all of the "Q" episodes (possibly excepting "True Q," which is only average), but this is the best.

"Conspiracy" - a ripping good yarn, and ... a big alien-gore finale in a Star Trek episode! The first time I saw this, I literally flinched and sat slack-jawed when Remmick's head exploded!

Least Favorites

"Shades of Grey" - looks like it was cobbled together to fill an episode quota or something ... the "lamest" episode in the history of Star Trek.

"Skin of Evil" - see notes in "Yesterday's Enterprise" above.

There are so many episodes in the other series that remain unseen by me, so I will abstain from delving into those -- with one exception:

Deep Space Nine: "Trials and Tribble-ations" - it's one thing to have a "cool" idea for a tribute episode, but it's something else to take it, and run with it, and really put in the effort and energy and talent to make it really, really, good. And they did it on this one.

Mark