I nominate "The Inner Light" as my favorite even given some of the structural problems with the story and the stretch of science plausibility that a race that couldn't save itself could create such exotic technology contained in the probe.
I think it rests wholly for me on Patrick Stewart's acting, such as leaving the bridge, touching the turbolift door frame like a man who from his perspective hadn't 'seen' it in 40 years. Or the way when Riker leaves him with the flute he clutches it with grief at the loss he's coming to grips with. And the music.
Yeah, cheesy perhaps - how much of Trek isn't really, but getting to live two different lifetimes, even if one was an illusion that only lasted 20 minutes was very intriguing.
The original series has to be "City on the Edge of Forever". To watch Kirk save the world and indeed probably the Universe and still lose so personally was something they really never dared do in those days. Except on "Bonanza" where if any of the boys fell in love she might as well get the loan of a red shirt from Trek across the lot because, man, she was a goner...
I never watched enough DS9 or VGR to have any opinion about them. I regard them as trying milk the idea of Trek for every last drop Paramount could get.
With "ENTERPRISE" which I seem to be in the minority having a fondness for, I'd say my fav is "Carbon Creek", though I loved the one where Archer had the amnesia and was cared for by T'Pol for years though I can't remember the name of that. I thought the show got really good in that last season with the Reeves-Stevens adding to it immensely but it was too little to late to save it. The writing before that 4th season was such crap.
I sneered at it when it first came on particularly thinking Blalock was nothing more than eye-candy, but she gave fantastic performances when she had some material to work with; my favorite is in the otherwise horrible Xindi season where she played an ancient version of herself when they meet the NX-01 from that alternate future.
I hated how poor Scott Backula was given an Archer character that was consistently written getting his butt handed to him by the alien of the week. It was a fantastic cast that just didn't get the kind of writing they deserved. I wish the show could get a do-over.