Interesting thread. Lets see.
1) Rachni queen - kill or release
I hate to say it but I'd kill her. The risk the rachni pose is too great. We tried to make peace with them before and had no luck. It took extinction (or so we thought) to end the war. Sure I could just take her word on it that they didn't want war and were forced by oily shadows... or I can do the only guaranteed safe thing and end the threat once and for all. I'd find it easier to endure the burden of killing one queen (even if its the last one) than I would facing the horrors of a Rachni War 2 and all the lives it will cost.
My Shepard always saves her, just for the record.
2) Balak - kill or let to escape
Kill Balak, everytime. It's another case of 'greater good'. This guy damn near slammed an asteroid into a planet... this is one extreme terrorist. Either save a handful of innocent people or ensure this lunatic doesn't escape to try this again. Saving the people would be the easier choice because its a simpler choice to justify. "Well, they're alive because of me, they'd most assuredly be dead if not for my choice." Where as killing him only gives you "think of all the people who you probably saved by making sure this madman didn't escape to continue his crimes."
Besides you're taking him on his word that he will spare them and not hit the detonator the moment he gets distance. Maybe the second he gets on his escape ship he hits the button. This guy was willing to slam an asteroid into a planet should I really be accepting his word when he says he'll spare a few hostages? He'd probably activate the bomb once hes on his ship and laugh about it.
3) Grunt - keep in a jar or release
Release. Keeping him in the jar seems wasteful. If you release him you might have to kill him - but so what if you were going to just keep him in the jar anyway. At least with releasing him you get the chance of him being useful, rather than just pickling on the ship.
4) Legion - activate, sell or keep for Alliance
I wasn't aware you could keep him for the Alliance. I'd activate him. He tried to communicate with us, even saved our lives (kinda). I'd be interested in speaking with it. Not to mention the whole N7-armor thing. Shepard's reasons for wanting to 'wake' it sound good to me. Worse case scenario we just have to destroy it.
5) Elnora - kill or let go
Kill. All eclipse sisters have to kill someone to get their uniform. She isn't innocent if shes wearing said uniform. Plus she made the poor mistake of drawing her weapon. To make matters worse, she's Asari. Think of all the people she could hurt in her lifetime because you let her go.
6) Vigo - kill or save the workers
Shame that Shepard only takes two of the squad and can't just split them up. I'd kill Vito. This isn't just some small time thug, this is the head of one of the biggest merc groups in the galaxy. It'd be like offing a mob-boss. Though, if I had more freedom with choice and wasn't stuck with the same choices Shepard gets... I'd split up the team.
7) Garrus LM - kill or spare Sidonis
Kill him. Everytime. Imagine if he was your friend, your ally. Imagine if he was part of your squad for two years. Then he betrays you all and gets the whole squad killed. This is a very real risk Shepard faces, really, since all the recruits are strangers and more than a little dangerous. A convict, assassin, bounty hunter, terrorists, a thief... Any one of them could had sold you out. What if it was your squad that were betrayed and killed? I sympathize with Garrus and would happily help him bring justice to the sonovabitch. Debt repaid, Sidonis.
8) Tuchanka - sabotage or cure
Sabotage. We need the salarians and their advanced warships for the war. Plus the krogan have done little to prove they've really changed any. I'd be fine with a cure if it was regulated or given only to Wrex's clan (assuming he is alive) but to give it to ALL krogan on tuchunka? Wreckless. Though I've heard some interesting arguments for the cure that have make me less certain on this. So who knows.
9) Rannoch - geth, quarians or both
Quarians. The geth sided with the reapers. No matter how much the story paints them the victim I cannot overlook that. Legion has drastically changed and is now asking to give ALL geth REAPER upgrades. The very thing that made them so dangerous to the quarians in the first place. If not for the reaper upgrades I'd be more than happy to 'spare' the geth. However since the only way to spare them involves them all getting these reaper upgrades... I just shoot Legion. The Legion I knew is dead anyway. Or at least thats how I'd justify it to myself.
10) Ash/Kaidan - accept to the crew or send to Hackett
Hackett. I need people I can trust to have my back 100%. Not someone who doubts me to the end and points a gun at me. Plus, Horizon. Now you know how it feels when someone turns their back on you. I'm vindictive.
Though I will say I'm uncomfortable doing this with Kaidan. I like Kaidan, I think he's a nice person. Horizon felt really out of character for him. Ashley I have no problem with because shes' a ****** anyway.