I'm finding that the second choices are the more compassionate and kinder replies for the most part on my Dark Side character, but sometimes it can be mean. Like for the Inquisitor quest where you have to interrogate an an injured Acolyte, the middle/second choices were the ones that cause the Lord/Overseer guy to make sure that he was safe, and transferred away after ratting out some apprentice. The second/middle choices also are what got me to help the Jedi prisoner in the Jailbreak quest, and get more Light Side points.