I think of all the games I've played, The Witcher series manages to do it best. There is very rarely an obviously "better" choice, and the game doesn't really punish you for making one choice over another: something that truly frustrated me about Mass Effect. You might get different gear one way or another, and the story is definitely different, but never objectively "better". The exception could be some of the monster quests (Adda in 1, Trolls in 2, etc) where there's the easy option of killing them for the reward, or the difficult option of helping them for a different, usually better reward, but even that balances effort and outcome really nicely.
On the other hand, in ME there is usually absolutely no benefit to most of the renegade options in the game, other than (in my opinion) a superior story, and for a lot of people that's not enough. Why the hell would anybody, for example in ME3,
<spoiler=ME3 Spoiler>Sabotage the genophage cure? Despite what you are told by the salarian, the EMS score of that outcome is substantially inferior. Is the story enough to make the choice viable? I think so: even with "perfect" outcomes up to that point, I see no future for the krogan except for an uncontrollable explosion in the population of a species which has evolved by necessity towards violence and aggression, the overthrowing of Wrex now his only leverage is gone, and a bleak future.
But the game doesn't present any particularly compelling arguments for the choice: it's sabotage the cure, be a monster, and get a worse outcome, or be a damned hero, ignore the stark reality of what you're potentially doing to placate a couple of your friends, and make everybody happy for plentiful EMS points.
This problem is quite consistent across the games: despite renegade supposedly being about doing dirty things to get the job done, the outcome of these actions is almost always worse than being a goody-girl paragon. That's not a moral choice: if you want there to be any reason at all to choose a renegade option, at least make it so the rewards are greater! Then players have a real choice choice: do you take the harder but "right" path, or the one with the greater outcome, at the cost of your morals? As it stands, the choice is go renegade, piss a load of people off, and get a worse outcome, or choose paragon, make everybody happy, and get a better outcome.
Aside from wanting a more compelling story, there's absolutely nothing even making players consider renegade choices. The Morinth/Samara one you mention is just plain silly: I can see some people disagreeing with Samara's Code but given a choice between her and somebody who has slaughtered hundreds of innocent people for her own pleasure, with her mind? Yeah... that's not a renegade choice. That's just suicide.
Anyway, on the Witcher, I really enjoy how things are framed in this game world.
<spoiler=Spoilers for Witcher 1 & 2>Everything's awful, and your choices are usually different flavours of awful and even if you want to do the right thing, sometimes there just isn't one. Do you turn the young elven woman accused of colluding with local elven... "freedom fighters"... over to the city guard, knowing she's likely to be raped and tortured, or let her go? And if you let her go... turns out she was colluding, and leads you into a trap where the "freedom fighters" try to kill you anyway! You can find her again after that: what do you do then?
Or in the first game, if you've been generally sympathetic to the plight of the elves, what do you do when a bank robbery threatens to turn into a slaughter? It's one thing to steal money, but another to kill people who are trying to stop you... and, best of all, staying out of it is an option for those who think both sides are awful!
That's how moral choices should be done, I think. Make it ambiguous. Don't stick stupid morality meters on things. Make each choice unique, with unique outcomes... that aren't objectively better or worse than the others.
