To sum up some examples. You can help a terrified woman find her way back to her home world after thirty years of wandering the Planes, investigate miscarriages of justice, help a kind but shy guard and a lonely but cheerful woman fall in love with each other, openly attempt to end Dakkon's life debt (which is slavery by any given name), confess and try to atone for murders committed by previous incarnations, redeem Trias, resurrect your teammates and willingly end your immortality, knowing you will end up in hell, which is better than having countless innocents die in your place.
Giving the nameless zombie a new zombie. She's just so sad that she can't remember her old it just feels like an immense victory to come up with a new one for her.
Despite all the horrible things you've done to them and can still do, you and members of your party can have a pretty good happy ending:
It's easily missed, but as you travel in the Fortress of Regrets you can gain the ability to resurrect dead... And cause enough mayhem to get the Transcendent One off your back long enough to raise each and every member of your party. Feels pretty good after powerlessly watching them die.
You also get a nice chat with each one and they reassert their will to help you. This troper always choose fighting over talking the boss to death because of this last discussion with your friends, at least last discussion "as yourself". That way they don't wake up after their violent death to see you have changed.
Bonus Points: with that last chat? You can FIX Dak'khon's mind and making him whole and focused again, and give Vhailor the biggest injustice to punish. Both of them become, because of that, nigh-unstoppable owerpowered killing machines, always a nice touch before the Final Boss.
And after the Transcendent One is dealt with: your farewells. Even better if you had the opportunity to talk to them BEFORE the fight: at least you had the chance to fight alongside each other one last time. You can say goodbye, thank them, apologize for what you've done...
And each of them shows his appreciation: "it's been a pleasure" from Morte, an silent declaration of love from Annah, the promise that Grace will find you again, settling your debt with Dak'khon... Even VHAILOR says something "nice", along the lines of "you're going in hell, but that's no meaningless punishment: use it to become better". Ignus, of all people, begs your forgiveness at having betrayed his "master's" teaching - and you apologise for your betrayal and then send him to the Elemental Plane of Fire, probably the one place he'll ever be happy and at peace without being a danger to anyone else.
It's a small moment, but Grace comforting the Nameless One during his Heroic BSOD after viewing the "Longing" sensory stone really tugs at your heartstrings.