The problem with the plague dilemma is that there were people in existence who did know the formula for the cure. As such, the fact that you can't get at it or otherwise force another potion out of someone is something that was clearly contrived to create a dilemma rather than a problem arising naturally.
A proper moral dilemma is something that arises more naturally out of the plot and without obvious contrivance. To use a semi-DD example: you find a new born baby that you know is destined to be the Demon Lord reborn, who will destroy the land if he is allowed to grow up. Do you kill a defenceless baby because of what he will probably become, or do you instead try to find someone who might be able to raise him in a way that will thwart his destiny?
Either choice looks bad. Kill the baby and you're gonna take a reputation hit like no tomorrow. Don't kill the baby and death & destruction is assured...
Sure, the game would need to play out over many years before that kind of dilemma was effective in the game, but it's the sort of thing that should make players really stop to think about what they're doing...
The witcher has a lot of great examples of proper moral dilemmas, but I don't want to put out spoilers for those who have not played it yet <img src="/ubbthreads/images/graemlins/smile.gif" alt="" />
