Wow, thanks for doing that much work. I will definitely be sticking to the episodes in the final list. Whenever I have time to watch more than a single episode a day, I will throw in the episodes from the first list.
And yeah, character arcs sound awesome, especially Bashir. A Dukat arc would also seem plausible.
I'm working on those arc lists; takes time, and I wanna do it right!
Looking back at my list, though, I'm really, really surprised that I didn't include "Necessary Evil." If you have to switch one out, I suppose I'd recommend ditching "Honor Among Thieves" in favor of "Necessary Evil," but then you lose what I believe to be the only O'Brien-episode on the list. So I say you should just add it in anyway.
I'm also surprised I didn't include "Waltz," or "The Collaborator," or "Things Past," though I think I decided early on to leave that category of episodes to be represented by "In The Pale Moonlight" and "Duet," and, to a lesser extent, "Honor Among Thieves" (killing three birds with one stone on that last one, being an Ambiguous episode, an O'Brien episode and a Little Guy).
This guy made up a list of all DS9 and TNG episodes with summaries and an assessment of each episode's essentiality to the show: http://www.reddit.com/r/DaystromInst...lgernoneplists
I'm pretty sure the number of his "essential" episodes far exceeds the 60-ish you had allotted, but it's still interesting. I don't agree with all of his assessments (for example, he's in the "'Nor The Battle To The Strong"-is-meh" camp) but it's pretty good overall. Actually, I just noticed that he feels that "Far Beyond The Stars" is not essential; just lost a lotta points with me, buddy. Bleh, I just read his review of "FBTS," and, boy, has it left a bad taste in my mouth...