TOS: Spock's Brain (featured on Agony Booth episode 1 - ok I'm done with the shameless plugs :p)
TNG: Shades of Grey
DS9: Run Along Home
ENT: Unexpected (will be on Agony Booth this week - ok now I'm REALLY done lol)
and worst movie...just to throw it in ST V: Final Frontier...COMPLETE $H!T
ENT: "These are the Voyages" For pure nerdrage, nothing honks me off more. Even the actors knew this was a stinker (some of the worst performances by good actors). They kill Trip...stupidly and pointlessly, they don't show us Archer's speech(!!!) and then they tack Riker's bit on the end which might as well have been "It was all a dream", it was so stupid.
also, disohonorable mention:
TOS: "Let That be you Last Batlefield" should have just flashed a screen with the words "Racism is Bad, stupid!" every 3 seconds. This was a real groaner and the padding throughout the episode of them running through corridors...oh, and people from Cheron live over 50.000 years...and can take over starships with their mind...and have personal invulnerability shields...holy wtf, Batman (yes, I said that because Frank Gorshin was in it). Blech! Most of the third season was weak sauce.
TOS: The Alternate Factor - Just bad, real bad
TNG: Shades of Grey - I generally dislike 'flashback' episodes at the best of times, this one was just far too tacky for my liking. Followed closely by 'Sub Rosa'.
DS9: Take Me Out to the Holosuite - I'm not the hugest sports fan, so to have an entire episode based around baseball didn't really work for me, that and Sisko didn't seem like he was the same charactor and the Vulcans don't seem to be acting Vulcan at all. Other than that, I generally disliked an Kira episodes.
VOY: 11:59 - Really really boring episode, I know many dislike Threshold for its dodgy story, but atleast it was mildly entertaining still.
ENT: These are the Voyages - Felt sick in the stomach watching this episode, was a complete insult that they said this episode was written 'for the fans'
As for the films:-
ST:Nemesis - The special effects were absolutly amazing, but the story itself really sucked, thankfully it had some awesome battle scenes to make it bareable, this is the only Trek film I've seen (I was at a premiere show) where people got up and left the cinema!
ST:V - Whilst many people dislike this film, I don't think the premise was that bad, sadly it wasn't as well executed as it could of been.