Dilemmas really only work (imo) if alignments are not 100% objective, writ in stone. Otherwise moral dilemmas are easy to navigate.
In my games there are numberless moral dilemmas. The best I can think of right now comes from a non-D&D game called Tribe 8 but the dilemma transcends setting as you will soon see.
The PCs are influential figures in a small community that is composed of exiles and banished members of a stronger, more authoritarian society. For some time they have lived in relative anarchy until a pseudo-religious figure attempted to unify them into a single community. In the ensuing strife another religious figure, a deeply disturbed individual (the lone survivor of a suicide cult) opposes this new unifying force, denouncing it as a fraud. At the end of the conflict, during which this dissenting prophet led followers into a violent uprising, the prophet's side loses and the prophet is taken prisoner. The dilemma? What to do with the prophet?
Keep in mind the following:
a. this society barely survives from year to year, holding her prisoner takes at least two people (the prophet and their jailers)out of the labor force needed to produce this marginal survival - running the risk of starvation.
b. exile or banishment is considered taboo by this culture due to the unfair nature of their own banishment. Also, the prophet lacks the necessary clarity of mind or skills to sruvive - banishment is a death sentence by starvation and exposure to the elements.
c. death, especially execution while imprisoned, would make the prophet a powerful martyr and cause considerable trouble in the long run by inspiring others to avenge their death.
d. Letting the prophet live would be considered an affront to the new unified community, and it would violate their nacent justice system, making the whole purpose of unifying moot.
Now, for fun let's move this into D&D by assigning alignments.
The original society is LE
The exiles are CN - with members who run the whole spectrum of alignments.
The unity movement is LG
The prophet is CG, with stronger emphasis on Chaos than Good. The prophet's followers are more CN, with some CE elements, but all are more Chaotic than anything else.
What's a PC to do?
In my game they ended up deciding to pull a Socrates - the prophet was returned to live out her life with her followers, and to commit ritual suicide. The remains were then given to the followers to dispose of in their own way. But the decision (played out IC) moved one player to tears. It isn't easy to hold someone's life in judgement when they aren't easily identifiable as 'evil', merely a differing politics.
This is what I see as a good moral dilemma. I know it isn't most people's cup of tea, but these sorts of decisions tend to elicit more thought than the usual sort of moral dilemma (do we side with the LE guy to defeat the more immediate CE or NE threat, etc).