Looking at the answers, I realize that I didn't agonize much when it comes to decisions in the series:
Whether or not to make Cole more human or more spirit (I thought more human was simply the best decision for awhile, but after playing Trespasser I'm conflicted)
That's the only time I was really conflicted, mostly because both paths give interesting scenes and dialogue, but in the end I decided that since the original Cole wanted to be a normal boy, then an almost-normal real boy named Cole would inhabit Thedas.
As for the others named here:
To kill or not to kill the Architect (I expect this decision to make some sort of impact in the next game!)
That never was such a big dilemma for me: killing the Architect, a sentient Darkspawn willing to parley and enter a truce Before even understanding What he is? I can play ruthless bullies, but incurious characters bore me to death, so the Architect always lives.
Whether to allow Avernus to live (with ethical experiments) or kill him
Didn't agonize either: my goody two shoes Warden left him alive and forbade unethical research (once again, incurious character = boring character in my book); my main, ruthless Warden happily drank his potion and forbade unethical research mostly because allowing human experiments were a PR nightmare waiting to happen.
Bhelen vs Harrowmont (I easily picked Harrowmont my first play through, but after seeing the epilogue slides I really doubted that decision... so I picked Bhelen the next time... and then I played the Dwarf Noble Origin and it made the decision really hard!)
Always choose Bhelen (never played a noble Dwarf Warden): the first time because Harrowmont approached the Warden with accusations that Bhelen was fixing ceremonial arena fights while Bhelen was accusing Harrowmont of bribing assembly members: went for the guy who seemed to commit the most venial offense. Ruthless Main, on the other hand decided to prioritize political expediency: the king most open to trade with the surface was the more likely to provide aid to Wardens on the surface outside of Blights.
To kill or not to kill Anders (it's easy to hate Anders, harder to decide if he deserves a quick death)
Kill.
My apostate Hawke was good friend with Anders, agreed that the Circle system was broken and deeply involved himself in the underground railway: giving Meredith the excuse to go genocidal on the Mages still in the circle was such a betrayal that I didn't picture my Hawke being coolheaded enough to do anything apart immediately murderknifing Anders.
choosing the Dark Ritual for the first time when I didn't know how the game ended or what would happen in advance
Refused the first time. The main Warden who followed would have agreed to almost anything that increased her lifespan.
Leaving Hawke in the Fade
I just can't leave him in the Fade.
Originally I was going to leave him in the Fade because I felt Stroud deserved more screen time (Hawke already had plenty in DA2) and because I liked the irony of having my lovable, snarky, idealistic DA2 protagonist dying for the Grey Wardens while my much more selfish Orgins' protagonist was still gallivanting around instead of doing her job.
Problem is my Hawke's an apostate.
Have you seen the Mage Hawke sacrifice? A swordsman attacking the Nightmare will look appropriately heroic, a mage trying to beat to death the Nightmare with his or her staff (instead of using their spells, in the Fade, where their magic is supposed to be at its strongest dammit!) look way too ridiculous for me to willingly inflict that scene to myself
Whether to kill or recruit Loghain
Always kill: goody two shoes Warden allowed his friend Alistair to duel him, so the question never arose, selfish Warden fought him herself, but certainly wasn't going to risk antagonizing her petlover who was about to ascend to the Fereldan throne.
Out of all three games only Well of Sorrows has been really difficult decision to me.
Mmmmmm... Weird magic pool that may inflict mind control on whoever steps inside... Let's let the weird hedge-witch take the risks.
Too many Quotes...