The thing is, I don't want to punish the player characters for doing the "wrong" thing or necessarily reward them for doing the "right" thing. I just want their actions to have an impact on the flow of the campaign. And and the end of the campaign I'd have an opportunity to tell them the long term impact of their choices. Does that sound like fun?
One thing you can do, at least that works for me, is to do things like play out in your mind the full impact of say, a given NPC being killed by the PCs, or the consequences of one of their decisions. That doesn't have to all be bad, some it might be good. If they are in a situation where they have a hard moral choice to make and choose A over B, both could have led to good and bad outcomes, but the important thing is the outcomes would be different and palpable to the players in some way.
If you want something more spiritual, then tying cosmology and mechanics can be helpful here (things like the Ravenloft powers checks leap to mind). But that is more in the realm of punishing players for doing wrong: though in fairness the powers checks as written give both a reward and a punishment to entice evil).
I think another thing is to give them real moral choices, where there is appeal to the bad choice. A good example might be in a game with magic, if a player brings a fallen PC to be resurrected, perhaps they have to strike some kind of terrible deal in order to get the resurrection, or maybe the available resurrection method is unorthodox and has some kind of evil result (which you don't have to disguise from the player, you can be upfront about what the choice is).
Not sure if this is helpful, but I do think making moral choices a part of play can be interesting. It is also an area of the game where players can get quickly irritated if you aren't all on the same page.