(Spoilers) If you do a lot of exploration and listen to a lot of the different conversations, you'll get a little "flash" and a brief sound-effect, indicating the game's acknowledging of going out of your way to do stuff. I think those flashes are an indicator of whether or not you'll get the option to not nuke the crap out of the Dark Ones. If you haven't explored enough or done too many negative actions (indicated by the game flashing almost black-and-white and giving you a lower, more ominous tone for the sound effect). The bright, positive flashes are a factor to getting the Explorer achievement, as well.
There's a LOT of "exploration" points, so I can't list them all. Off the top of my head, I do know a few things that you should avoid so you don't get the "negative" flashes.
1. Exhibition Station, there's a guitarist by a little campfire playing for some people, with some bullets nearby. If you steal them, you'll get negative points.
2. Riga Station, at the bar, there's two guys discussing some shady "merchandise" (which could either be drugs, or women, or whatever). If you stand next to them too long they'll stop talking and look at you, and ask you to leave. You'll get negative points for it.
3. In the "Ghosts" chapter, shooting the child's skull in the ghost train (the silhouette of the child being chased by the nosalise shadow encounter, the kid's skull is underneath the train seat near a bloodtrail). Also, shooting at the ghost train as it passes will net you negative points as well.
4. In "Anomaly", shooting the Anomaly when it comes close to you and Khan will get you a negative reaction. Inversely, if you stay close to Khan and don't run ahead, you'll get some positive flashes after he asks you the question "So, you feel it too?" or something like that. And right after, if you don't run ahead you'll be treated to an anomaly killing some nosalises on the tracks to the other side of you, prompting Khan to go into his spiel about how the anomaly is "no more evil than, say, fire. It just depends on your point of view." giving you some more positive points.
Uh no...you do not get that choice unless you played through the whole game the correct way. If Khans voice doesn't come into your head and whisper to you at the end, you do not get the choice to destroy the laser.