Well, people have said this already, but there is a big difference between Bioware when it came to how good and evil is portrayed throughout their games.
Star Wars: Knights of the Old Republic and it's sequel pretty much had to be about a straight line between good and evil, because really that was how George Lucas envisioned it, and who is Bioware to conflict with the original vision of Lucas? (A lot of you might say otherwise but I'm just saying) No "Expanded Universe" writer as they are called can write anything about Star Wars without George's say so and approval that it fits into the story and the overal philosophy of Star Wars. The man put a TON of allusions to the Bible and the Judeo-Christian ideology throughout the movies (i.e. Anakin is born to his mother with no trace of a father and has the whole "Chosen One" thing so he's pretty much Jesus in Star Wars form, the dark side is all about temptation and fear to gather it's followers and so too is the devil and all of his evil ways, and a whole bunch of other comparisons that I can say, but I won't waste time here with preaching

)
Even with Dragon Age, one really can't escape the whole Christian morality factor entirely. In Dragon Age, you have a choice to contaminate the ashes of Andraste (which again, is a mix between Saint Joan of Arc and Jesus) and as soon as Leiliana finds out, she chastises you for doing something unspeakable, i.e. you may not believe in a God or Gods, but regardless, you have just deprived millions of people who do believe the chance to behold and venerate those ashes, so aside from the act of being sacreligious, you have in essence stolen something of BIG importance from the people who want those ashes because they truly believe. And then Leiliana tries to kill you for it out of her fervor and sadness over the act.
Mass Effect really only has Biblical references in the form of names (i.e. the Lazerus Project, Christ raising Lazerus from the dead, and the Geth, Legion, who is named after a passage where a demon identifies himself as such because he is many and not just a singular demonic entity, and that he corrupted a man and yet again Jesus saves the day, excorsises it and the demon runs off and finds another host to possess and it possesses an entire herd of cattle and they all run off a cliff, but in the end one of God's flock is saved.)
Ok, going away from the Bible now.... (I know some of you may not like it when people talk Bible, so I'll just move on.)
With Jade Empire, I found it very hard to see the whole "ambiguous morality" mechanic with the Open Palm and the Closed Fist, they just seemed like another way of saying Good and Evil again when I played through the game (I mean as an example, killing people for no other reason than they are in you're way just seems plain evil to me, not really a "they are weak, I am strong" sort of thing in my eyes) But I do see the concept of it all, one is a "serve the masses no matter what the sacrifice to ones self" and the other is "many are weak, serve only the strong and yourself and it will make you and inspire everyone around you to be stronger"
Mass Effect plays this concept a bit better with the Paragon and Renagade options, in those games I had a much easier time of seeing the different Altruistic and Machiavellian paths of acting towards others. But some points in the game just felt like they were borderline evil: like the time where you go up to a Batarian gunship mechanic in Omega, and you can kill him with his own electric wrench thing, that to me was evil. A "Renagade" option would have been to toss him around a little bit and intimidate him to run away, not kill him outright.
So in short, I do believe that Bioware does a good job with portraying Good and Evil, however I am not too keen on the whole "ambiguous morality" thing, I get enough of that in the real world, I go to games to escape that not face more realism in morality! I suppose I just don't like the fact that life is nothing but shades of grey, and that I wish it was more black and white so that the world would be easier to help out.
Sorry about this being so long, I think a lot about these things in my spare time, pathetic I know...