I have an entire game where even to this day I find evil choices impossible to make on it, and that game is Steambot Chronicles. The characters in it are so incredibly endearing that I can't possibly deliberately cause harm to any of them, or ignore helping them, except the bad guys of course.
[Spoilers for Jade Empire]
For a specific evil decision, I'm torn between two as to which is worse, and they are related. In Jade Empire if you want to be evil you can bind Death's Hand forcibly to your service to get him as a party member, which in and of itself isn't difficult to do, it's the consequences of doing so and getting your new party member that are difficult to deal with. As a result of keeping Death's Hand, every party member that disagrees with doing this becomes binded by you as well, taking away their free will (though sort of alternately you can free Death's Hand at this point, but what sane person would actually do that?). As a result they hate you with a passion for what little is left of the game, which is heart wrenching, even more so as it combines well with the next choice. Almost directly before the final fight, you're asked whether you should destroy the Water Dragon's body or poison it with human blood so you can become a god after beating the Final Boss. Either way cuts off the Big Bad's power supply, and so MUST be done, but if you choose to poison the Water Dragon, your party members that objected (or would have) with Death's Hand previously object again, and they regain their free will and fight you, and you have to kill every one of your party that isn't still on your side, incredibly heart wrenching, depending on how much you cared about them, and Jade Empire does a pretty good job of making you care. By the way, this choice is the ultimate of good or evil choices in the game, this can either completely invalidate or permanetly reinforce every choice you've made up to this point.
Another Jade Empire choice which deserves a mention is the choice of which one of 2 demons possessing a little girl that you back, and which one you fight against and banish. Choosing the evil one means that you condemn the little girl to life as a puppet, only crying and screaming just before the evil demon talks, even a completely black heart can't avoid feeling pity for that girl.
I don't know about the rest of you, but for me these choices impact me so much not only because the characters are so endearing, but because there is no third option, especially since I find myself really wishing that there were, and I've probably thought up a couple for each as well.