For my money, the best dark choices tend to be ones that are fairly justifiable. For example, in Dragon Age there is that kid that is possessed, and there is a blood mage that can open a portal so you can save him. The mom offers herself as a sacrifice in order to power the portal. Now you can sacrifice the mom to save the son, or you could even kill the kid. I thought both were dark choices without being simply evil. They both had the greater good at stake with choices that were less than ideal. Apparently there was a good choice, going to the mage's tower, but the situation seemed more urgent than making a long trek with a possessed kid to me.
So far TOR seems to be giving those choices on occasion. There is a flashpoint video aboard a ship (Esselles?) that shows the players choosing between spacing the engineering compartment to put out a bunch of fires or running around trying to put them all out (or some other lengthy task.) It makes perfect sense to sacrifice a few lives to save the rest of the ship, but it is still a pretty dark choice to make. A lot of these light/dark choices in these games that I consider difficult tend to be more about being fast and effective or being slow and careful. The 'kill this guy for fun' stuff is boring.