In Mass Effect 1, choosing between Ashley or Kaiden on Virmire, when one of them has to stay behind and detonate the nuke. It's not as tough a choice now as it was back when I first played it (then it was agonizing) as I've played ME1 at least 8-10 times over the years.
The Dragon Age games had several tough choices to make, though I can't seem to bring any to mind right now. Wait, there was Solas's personal quest in DAI, where you had to save Solas's friend (who was a spirit from the Fade) which was summoned against it's will by a group of mages and turned into a demon which would attack you, and you don't want to kill it because then the Solas's spirit friend dies. But there's a way to avoid that once you figure it out. Once that problem is dealt with, you have to deal with Solas's anger, as he want's to kill the mages. So you've got a moral choice to make: allow Solas to murder the mages, or to convince him not to kill them.
The Witcher 3 also has many tough decisions to make in some of the quests, and most of them don't have a right or wrong, or good or evil choice. I think one of the toughest ones was at the end of the Bloody Baron questline, where you had to choose between saving his wife Anna or rescuing the orphans. There is no happy ending there, you just have to go by your own moral compass.
Honestly I think it was Yennefer or Triss. I chose Yennefer.
Years ago back when I first played Witcher 3 on GOG, I went with Triss. This time, in the Next-Gen version of W3, I went with Yennifer. I think I was partially influenced from reading all the Wicher books last year, and many of the character personalities stuck with me when playing the game.