My thoughts: (disclaimer, I only got to page eight before I had to say something, lol.)
About the Collector Base first: Destroying it is the only logical option, why? Reaper Tech is proven to indoctrinate, this is fact, even small amounts cause indoctrination. ME1, Saran as first example of this FACT, Cerberus op using dragon's teeth now known to be reaper tech lead to the death of the team/indoctrination and husk-ification, disabled ship in side quest reaper tech crew indoctrinated, and Salarian STG team members captured and held for only a few days to a week, indoctrinated. ME2, Mine with reaper tech in it, miners indoctrinated and husks built by the tech; a dead Reaper indoctrinated the team sent to it, and do I honestly need to bring up Arrival?? All facts point to this one out come.....a fully functional Collector base filled with active Reaper tech will lead to indoctrination!!! There is no reason to keep it, it WILL indoctrinate people; that's what even "dead" Reaper tech does, why wouldn't active Reaper stuff?? Even if you trust Cerberus now to have the best intentions why would you trust a base full of Reaper tech not to indoctrinate them?
The Council: I can give that as being either or, it really depends purely on personality, both options hold weight. Renegade = must stop Sovereign so need to save ships for that; Paragon = when this is over we need stability, a standing council will be able to give that better than a bunch of green councilors. It can go either way and those are only two possible ways to think about it. Without meta-gaming there is no right or wrong and both are logical.
The Rachni: A big part is once again you as a person. Meta-game says having the Rachni against the Reapers will pay off but even then its a gamble. It's purely up to you as a person, there is no right or wrong and both can be justified with logic.
The Genophage Cure: Keeping it and giving it to Wrex to use as he sees fit (which my guess would be small doses to Urdnot females) is the most logical option but we don't have it in ME2 (I think we might in ME3 trough). Baring that, destroying it makes sense, but it's up to you. Do you trust Mordin, then letting him keep it is a good idea too, which I do trust him so I let him hold onto it to decide what to do with later.
Veetor: The only info we need from him is the data on the Collectors and how they capture the people, all of which we get from Tali before we leave, she gives us, right then, his omni-tool data. There is no reason to hold a sick traumatized man.
The Geth: This is a hard one. Honestly, I don't see either option as really being paragon. You are either killing millions of geth or basically brain washing them and removing their free will. No wonder Legion was undecided! I rewrite for a simple reason, if you kill these heretics there may be more off base who could start back up again and rewrite Legion's geth later. If you rewrite then those geth not on the heretic base will link up later and also be rewritten. That's my logic for the rewrite.
Garrus' Loyalty mission: I personally wouldn't let a friend become a murder. That's just me, maybe your a terrible friend who doesn't care about a person's long term mental health but it is proven fact that something like 90% of people who kill out of revenge or anger become mentally ill after years of struggling with what they've done.
Anything were you kill a criminal: I'm a Spectre, I serve the people and the law. For me that means due process. Capture if possible, kill only if I have to, release them if I can't bring them to proper justice now for lack of evidence. Sorry if think that's dumb but if you don't like that then I'm glad you don't have a hand in writing our real world laws or my uncle would be dead as he was falsely accused of a murder...you guys would have killed him as he was the prime suspect all the way up till the real guilty party confessed after being arrested for possession of a narcotic. And in the real world a person like Shiala who was basically drugged by a third party would not even go to jail for what they may have done while drugged (note if she had taken the drug willingly she might, might, face some punishment that is almost as bad) let alone be killed for it. But you may also think being a Spectre means you are like a Judge from Judge Dread; and you weight the evidence and think the punishment fits the crime; so there is some logic for doing it, still it seems wrong to me based on the way the real world works.
Interrupts: Just do them, or not. I do some, shooting the mech (i don't even get this, it's not a person why is it renegade?) on Garrus' recruitment mission, shooting the Eclipse mercs on Miranda's loyalty mission (I do it cause they've made it clear I'll have to kill them any way), but for the most part I don't. Like punching a certain stupid reporter, I don't because I'd rather make her look stupid with logic and facts then give her a legitimate reason to have a smear campaign launched against me. But to me the interrupts are there so I as a paragon can be a jerk every so often or you as a renegade can be nice a few times; they don't define you to the core like the dialog option do which only unlock as you build your personality while interrupt are available to everyone. So do it if you want to.
The worker's on Zaeed's loyalty mission: I save them, and to me it makes the most sense. However, I go into it only if I can talk him down, he risked the mission, as my Shep says. It's about the mission and that was saving the factory from the Blue Suns, not killing some random (to me anyway) guy. Someone not caring that a bunch of innocent people will BURN alive is not renegade, it a sociopath. Zaeed is admittedly a sociopath, my Shep is not.
The Greybox: I destroy it, it's only logical, it's what he wanted so Kasume knows its what's right too.
There is more but I feel like I may have said enough (or too much? lol) so I'll stop now, if you read it all then we can talk and I'll address legitimate disagreements, otherwise that's fine; but I think all my points are valid.