A few personal favourites:
The Drifter - Hyper Light Drifter
Guillo - Baten Kaitos Origins
Skull Kid - The Legend of Zelda Majora's Mask
K - Virtue's Last Reward
I... huh. There's a very obvious trend here that I didn't even realize I liked until I saw all of these next to each other. I'm also generally a fan of bird-like heads/faces, so I like the Yukes from Final Fantasy Crystal Chronicles, and characters with plague masks, like Eileen the Crow or Plague Knight, as well as very clean-looking mechanical things with lots of moving parts (think Atlas and P-Body from Portal 2, or Sam Gideon from Vanquish).