I did not send Jana to the Wardens because I'd already had that 'Wardens Acting Weird' vibe/convo from Hawke/Leliana/Blackwall. 'Now is really not the best time to join the Wardens. Sorry about that. (not really, you'll thank me later).' The one time I didn't actually have an option where she agreed she wouldn't join them afterward, I still didn't pick the 'Sure, do whatever' option so it was that same poor senior warden (which really irritates me anyways because come on, Clarel! You honestly aren't even thinking at this point, are you?).
I felt poorly that I accidentally got Ser Barris killed in 'Champions of the Just' my first time through. I regretted his death at the time and suspected it was optional, but actually having that confirmed made it worse. I also regret that choosing to rescue the Templars puts Felix in a bad spot--as does not even going to Redcliffe. Yes, he's dying anyways, but I want him to have that moment with Alexius.
I did not feel badly about rejecting the Qunari alliance by saving the Chargers, but I did feel for the Iron Bull. I feel like the decision to become Tal-Vashoth isn't even in his hands...and it should be. Did he technically give the Inquisitor command of the Chargers? Yes, but they're still his men. He should get the final say. But that's my opinion, and I'm not interested in evilly moustache-twirling dictatorship Inquisition where it's the Inquisitor's way or you can hit the road. xD
Hawke staying in the Fade, sacrificing himself for the rest of the team, is just such a good, truly in-character moment for my canon Hawke that it was a beautiful story moment for me. The Hawke paired with Loghain? Also in-character for him. The Hawke paired with Alistair...not so much, unfortunately.
While I think Cole as a spirit is more to Cole's liking...It's still so sad if you have certain conversations in a certain order and he can't handle remembering the 'real Cole.' 'Forget.' "...Cole?" 'You can still use that name if you like.'
But the worst moment for me, by far, was when my Pro-Circle/Pro-Chantry/Pro-Templar!Mage!Male!Trevelyan told Cullen he just needed to suck it up and take his lyrium. Even he sort of came to regret that. And it kept coming up. It was just terrible. A part of me loved it because it was a good story, but it wasn't at all what Cullen wanted and I knew that going in. But that Trevelyan just didn't understand why Cullen was trying to force a blind spot where his duty was concerned--at least, not at first.