The Original Series, for me, veers from being some of the best television I've ever seen, to some of the worst.
That said:
TOS - Space Seed. Not just because of Khan either. It's a damn good episode.
I'm also a fan of Balance of Terror and The Doomsday Machine, among others.
TNG - Chain of Command is my favourite bar none, even if on subsequent watches Riker looks more and more like a dick. Not that Jellico was right, mind you, but he wasn't totally wrong either. And David Warner ****ing kills it as Madred. I also think it's Stewart's best performance in the series.
I like episodes from every series, but I'm particularly fond of The Offspring, Yesterday's Enterprise, The Drumhead, Measure of A Man, Q Who.
DS9 - In The Pale Moonlight. It's not just dark. It's believably dark. Sisko and Garak are amazing, and it's a massive turning point in what was a brilliant arc.
As it's my favourite show, DS9 is going to have most of my favourite episodes, so really, I like most of them. Special mention goes to Sacrifice of Angels though, purely for the spectacle of it all.
VOY - Scorpion, probably. It's one of Chakotay's best episodes, and is the introduction of Seven, who to be fair is one of the best characters in the series. I like Message in a Bottle too. Andy Dick might be a **** IRL, but he plays the role of a more annoying EMH perfectly. Worst Case Scenario starts off as one of my favourite episodes but falls apart once the malfunction happens, I feel.
ENT - The Expanse. Just a great episode from top to bottom, and set the tone for a really solid-to-great season of Star Trek.
I like most of seasons three and four, but anything with Shran in it gets my vote.
DIS - As poor as I feel the show has been, there have been some good moments. Pike especially carried a lot of episodes from mediocrity to a point of actually being somewhat enjoyable. I am hoping the show grows its beard in the third season, though.
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I tend to like a lot of the screwy, one-off episodes. Anything with parallel universes is good with me. And episodes like Genesis in TNG (the one where they all devolve and Worf tries to eat everyone).