Also re: TNG PD
The point of letting the entire culture die as seen in "Brothers" Their point was "Who are we to decide who lives and dies, since we can't save them all"...I think that's pretty dumb in the end. I see what they're getting at, but you pick some and do what Worf's brother did.
As far as "Penpals", Does Starfleet REALLY let entire civilizations die from natural causes when they can save them without even interfering??? THAT'S beyond the pale. I agree entirely with the spirit of the convo they have (though it's dumb that they have it. This is the PD, every person in that room took course upon course on the subject, and Picard has to take them to Prime Directive 101) but the conclusion "We arn't even going to look into the matter" is wronnnnng.
As for The Apple, when Spock has misgivings, it isn't a slamdunk.
edit: I'm coming around on whether or not this is a PD violation. I don't think they have a culture. I THINK it's 30 guys in a lab experiment. And if there is no culture, but just 30 really intelligent ants mindlessly feeding a snake-head, and putting make-up on each other in their off time...and if there's no culture, how can there be interference?
But I do strongly disagree with the ultimate fate of these guys, and some other nitpicks.