There are a lot of obvious ones I could pull from, but I'm going to go to one that nobody will probably mention- Saren Arterius from the first Mass Effect. Sure, he's an Antagonist, granted, he was a violent ends-justify-means psychopath prior to the tragedy I'll be bringing up, but... Indoctrination. In just about every conversation and every fact I find out about him post the intro questing on the Citadel, I feel more and more sorry for him, similar to how I feel for Matriarch Benezia (and just about anyone else that ends up indoctrinated because they thought they were doing the right thing).
Especially pronounced in the conversations on Virmire and the finale if you take the right line of dialog. He knows it's bad, and thought he was doing the right thing, but he's being influenced, and starts to know it, it's just... I felt bad for him. Props to the voice actor and animations team for conveying that emotion.