I just think a bad way to go about evoking feelings in a player is by having a mute. I think relatability is one of the biggest factors personally, and the manipulation of the environment with lighting and such. I also like a character that makes realistic choices although admittedly it can be difficult for this to work as the game can become boring.
I think one of the oddest games for the way it made me feel was Portal. I felt kinda...sorry for GLaDOS...which was weird because they're the main antagonist. I also felt betrayed by a computer which is just nuts. Valve are really good at that kinda thing which is partly what separates them from other companies.
That's why I fell in love with Portal. Portal was the first source game I played, and it drastically changed the way I saw first person shooters (if you can call it a shooter). The game wasn't just about shooting portals on walls and knocking over turrets. It was like you did what Glados said because you trusted her, and when she tried to murder chell in the fire, I trusted Glados so much that I actually waited a bit to see if someone/something came to pick me up. When it didn't I felt sorry that I had to escape, and I felt even worse when I killed her and saw the cake, and then she sang still alive... Short, simple, yet amazing game. I can't wait for portal 2.