Ok, OP here. Read the replies and thought I should give my two cents on the options and why I thought they were important.
Save/Destroy Rachni - As someone previously has mentioned, it's that doubt, that feeling that the queen might just be lying to you, that you are releasing something that may become a bigger threat than Saren (you didn't know what reapers were at the time).
Save Ashley/Kaidan - Personally, I liked the two characters. I don't see Ashley as racist, just inexperienced with alien relations or ignorant, at the worst. She doesn't actively hate aliens, she has her doubts, which is understandable given her family background. Kaidan has a right to be a whiny *****, because his childhood has been mostly ruined by those in power, trying to push and control him to become a good little soldier; a much milder version of Jack, in my opinion. And as someone else has previously mentioned, it narrowed down to who was your love interest. If you wanted to have a romance with Ashley/Kaidan, then you would be saving that person for selfish reasons.
Save/Abandon the Council - Really just the question of unity/solidarity, between all sentient species or humanity. Since Cerberus was a big point in the second game, I see it as having significance.
Allow/Dissuade Garrus from killing (both 1 & 2) - I believe in a difference between justice and vengeance. Garrus was pursuing vengeance, in the guise of justice for others, which discomforted me a bit. I am a bit surprised that not a lot of people doesn't feel this way, actually. In hindsight, I could've replaced this one with something else, huh?
Rewrite/Destroy Geth Heretic - Well, you know the reason.
Save/Destroy work on Krogan genophage cure (in Mordin's loyalty mission) - Again, you know the reason.
Samara/Morinth - This is interesting in two ways to me. First, as a paragon, would you be comfortable with a warrior priest with the strictest of dogmas trying to kill someone (albeit a serial killer) for a birth defect? Second, as a renegade, Samara actually mentions that she would kill you without a doubt if she were to meet Shepard after the Reapers based on her actions. Would you let a killer live to save your own self, given (what seems to be) your only chance?
Save/Destroy Reaper base - Well, you know, the loss of humanity for power, all that stuff.
Also, for those mentioned:
Tali's trial - I can see how hard the question is, whether to expose a certain and definite crime or say nothing to save a comrade from shame? To be honest, if anything, I thought people would be about persuading the quarians to make peace or go to war.
Side mission on euthanization - Granted, I never thought about this at all. I thought this was pretty straightforward, what with the man facing certain death even if he were to float through space (since power/nutrient/oxygen would run out sometime in the future). But if that factor was left out, then yeah, sure, it's a question worth asking. Since there was nothing to suggest the man's opinion on the subject, or a signed DNR statement or something.