The Sisko PALE MOONLIGHT ep definitly deserves mention, the last few lines
The thing I liked about DS9 was that it showd two things:
1. What people who didn't live in the UFP Utopia had to go through and how they resented it (eg Eddingtons speeach when he defects to the Maquis) (and when Sisko is talking to Kira about the average Federation persons opinion of the Maquis "the problem is earth, on earth there is no war no poverty and no crime, but out here all the problems havn't been solved yet")
2. It explored what would happen if the very existance of the Federation was threatened from the time Bashir said in past tense "if something disasterous were to happen to the federation would we hold true to our ideals or end up here...right back where we started?"
They didn't quite end up back in the shithole 21st century, but they did violate their own principals when their very existance was in danger, I'd argue that if their very existance is in danger it was justified, but it showd that when your not on a Galaxy class starship cursing around the utopian federation the world is one big shade of grey, thats what DS9 was all about.
Picard had a similar chance to make a similar decsiion with Hugh and he coudln't do it, I personally would have, I wouldn't consider it Genocide since your never going to be able to pull a 7of9 on every borg and free them all, and you could argue they lost their individuality when they were asssimilated.
I know alot of fans hate that episode for the reason of sacrificing principals, but rightly or wrongly that happens in wars, even fake psudo-wars where the existance of the state is not threatened like the war on terror the USA, an adminable country in many ways, pissed all over it's own constutition, these things happen.
No matter how far we evolve in 300 years, if the very existance we hold dear is theatened (as it was in the Dominion war) we'd go to extreme measures.
TNG:
Dramatic: Picard playing the flute at the end of "Inner Light." Heartbreaking!
Funny: Sir, I protest! I am NOT A MERRY MAN!
What I liked better in that ep was when Geordi was playng the banjo thing and Worf calmly walks over, shamshes it in two, reuctantly says "..sorry" and hands it back to him.