****SPOILER ALERT****

Simple question really, have games ever made you question your in-game motives? 

I have some, but most of the games that try to make you feel sad for what you did (like learning you were bad the whole time) just don't affect me. Other games though, manage to hurt characters that you come to like in some way, and usually it's caused by the player. That's what gets me: 

- Shadow of the Colossus: Can you honestly tell me you laughed when you downed some of those peaceful beasts? They're minding their own business and then you come up and stab them in the face. Not cool!

- Metal gear Solid 3: Snake Eater: Having to shoot Big Boss at the end, there's nothing more heart throbbing then literally having to press a button to end your helpless mentor's life. 
And The Sorrow's Boss battle where you had to pass through all the souls of the soldiers you killed. It took me minutes, oh did I feel like a douche.

- Running over/shooting random civilians in GTA, it isn't always fun. Sometimes I try to drive like a normal person around the city. Get's boring after a while, though. 

Yours? 

Ironically I just read this article here relating to the subject. 

Are you kidding, I got into first person view to run them over!

I admit it is fun the first few hours.  

Everyone in GTA is dumb as hell, so i didn't mind killing them

but recently its Heavy Rain , everyone who got it knows the trials.

Betraying Alistair to get Teyrn Loghain Mac Ti in DA:O.  I actually felt kinda bad.

It's always fun, I love being being cruel in video games. I ALAWYS go for the most brutal options.

I don't think of anything big, perphaps because I rarely play deep games

one thing I never liked is when I was playing chrono trigger, and I was trying to save Lucca's mom from the machine, and I couldn't, she was eaten by the machine. I felt so bad, luckly I did it on my second try

It's so bad killing Felynes / Melynxes in Monster Hunter 3. They're not real cats, but they make all the right noises. Sometimes I kick them, just to see how awful I can feel.

I just can't shoot wookies or ewoks in star wars battlefront. I'd rather let them kill me instead lol.

It's been a long time I played FF Tactics Advance, but I seem to recall Marche saying and doing things that made me think, "Is this really my main character? Is he supposed to be my hero?"

And I liked this one, from the comments in the OP's linked article:
"the most obscure thing i can think of was when playing max payne you hear some guards talk about films, and one of them really knows his stuff and seems like a cool guy i could have got along with, but alas had to go chow yun fat up in his shit but i still felt really bad about him"