Going back to start...
"Cogenitor" - It's easy to see how Trip loses sight of things. I can sympathize with his position even as I disagree with it.
I actually find this one a bit crazy. The chief engineer and his wife were treating Charles like garbage. Trip made Charles aware that she was being treated like garbage. But when Charles refused to be treated like garbage anymore, the blame is laid on Trip.
"I, Borg" - I still doubt the weird little graphic would have done substantial damage to the Collective, but the question of whether Hugh should be sacrificed without his consent in an effort to destroy a relentlessly hostile foe is well-handled here.
"In the Pale Moonlight" - Sisko not only faces an ethical dilemma that he arguably fails, but he can't even share what he's going through with any of his usual sounding boards. In the end, the dilemma is effectively taken out of his hands in a way that only digs the knife in deeper.
These two are opposite sides of the same coin. Picard and Sisko are both in a position to do a deplorable action for a greater good. I am of the mind that Picard chose wrong. Perhaps that is to my shame.
"Tuvix" - There's entire threads discussing this one. I doubt I can add anything. I'd argue the only weak point, which isn't the fault of the episode itself, is that the entire event is never referenced again throughout the series.
Naomi mentioned it once, while many controversial events weren't mentioned at all. But that was Voyager: Reset button, reset button, reset button, ad nauseum.
"Dear Doctor" - I want to like the handling of this one, but the poor science makes it problematic.
Archer invokes the worst aspect of the Prime Directive before there's a Prime Directive to invoke.
"Homeward" - Perhaps one of the worst handlings of the Prime Directive; I don't recall Our Heroes even particularly discussing whether they shoulld be trying to save what they can of the Boraalans?
When Deanna snootily said that "the Prime Ditective was created to ensure non-interference", I wanted to smack her.
Had I been in Picard's shoes, I'd have beamed up Boraalans until my transport coils burned out or I reached the ship's life support capacity. Then, jetted them off to a new home, and if Starfleet later court martialed me for SAVING THOUSANDS OF LIVES, I'd head off to New Zealand with a smile on my face.
Insurrection - The epitome of raising some complex moral arguments and then burying them under an action-adventure film.
Didn't bury them deep enough. I could not force myself to root for the Baku.