Doomsday Machine from TOS is one of my favorite Trek episodes; the tension packed into that episode is brilliantly thrilling, even today.
Where Silence Has Lease holds a special place in my heart. One, for a more frank exploration of death that Trek sometimes lacked and, two, for the fact that Nagilum freaked me out
as a kid (still does a bit).
I like A Matter of Perspective, courtroom dramas are fun and I thought this one was rather well done.
Clues is another fun, "What the heck is going on?", episode that invited multiple viewings. Conundrum follows in its footsteps.
Duet. One of the best of the early DS9 episodes. Great character building for Kira. Same goes for "The Wire" for Bashir and Garak.
Civil Defense (seeing Dukat so flustered is great) and Our Man Bashir (I'm a big Bond fan) are fun episodes as well.
Haven't watched much Voyager or Enterprise lately. Looking at the Memory Alpha lists aren't jogging my memories sufficiently.