Letting
Shiala and Rana Thanoptis go
For both of those, my Shepard let them go because he's a soldier, not an executioner. Also, he really didn't see them as potentially serious threats. If either of them had seemed like they were masterminding some aspect of Saren's plan, he might have thought differently, but in both cases they just seemed like they had gotten in over their heads.
Saving the Council
For my Shepard, the council was an important figure for galactic stability. While he might have frequent dissagreements with them, he believes that they will be necessary in the coming fight with the Reapers. If the human fleet left the Council to die, he probably wouldn't be able to get support from Turians, Asari, or Salarians, which, in addition to being the most influential races, are also the races with the most military might.
Destroying the Collector
Base
This decision was more because he didn't trust the Illusive Man to use the technology ethically. He already knows that the Illusive Man is willing to sacrifice large numbers of humans for what he consider the best interests of humanity, which are distinctly different from what Shepard would consider them to be. While he might gain a slight edge against the Reapers, the consequences of giving Cerberus that much power were too great. Plus, Miranda was with him, and even she didn't think it was a good idea to keep the base.
Letting the Rachni Queen live
This was a tough one for my Shepard. Since humanity wasn't involved in the Rachni wars, he didn't have the same innate prejudice against them that another race might, but he was still aware of how other races felt. Ultimately, he felt that killing the Rachni Queen was essentially an act of preemptive genocide, which he just couldn't do.
Hiding the evidence at Tali's
trial
For this one, Shepard had to decide which would give Tali more closure: protecting her father and being exiled or betraying her father and being aquitted. He decided he'd take Tali's word for it that she could handle being exiled, but not seeing her father posthumously branded a traitor. Then, when they got back to the trial, he figured he had nothing to lose, so he threw the Hail Mary and called the Admirals out on their ulterior motives.
Rewriting the Geth Heretics
This was another tough one for my Shepard. On one hand, he has years of experience telling him that any synthetic capable of independent thinking will reach the conclusion that organics are unnecessary and decide to annihilate them. On the other hand, Legion possibly saved his life on the derelict Reaper, volunteered for his mission to help a bunch of human colonists, and outright telling him that the geth he faced previously are not true geth, all of which means that there is more to the geth than Shepard previously understood. Therefore, he has no definitive answer about the possiblity of future coexistence with the geth.
So then, it just came down to a choice of possibly strengthening an ally (with the risk of strengthening an enemy) or possibly weakening an enemy (with the risk of weakening an ally). Ultimately, he figured that since the true geth were definitely opposed to the Reapers (otherwise there would have been no split in the first place) and seemingly indifferent to organics (they've stayed in their own part of the galaxy for 300+ years), their value as an ally outweighed their potential threat.