I guess that most games use the same elements as movies: the story, the pictures and the music.
You've mentioned
Half-Life 2 and I think it just uses very basic methods: a good looking female who's obviously interested in the main character is enough to touch most typical (male) gamers.
The fact that she's made of pixel doesn't really matter: comic books or animated movies can cause emotions even if the characters are obviously not real. It just requires a bit of work to make her realistic enough (for example facial expressions and voice acting). I've heard that a lot of work was done in
Heavy Rain to get realistic eyes since eyes carry a lot of emotional content. But even then I'm not really sure that it's required: older games such as
Dreamweb could also carry a lot of emotional content with low tech and few pixels.
The fact that the main character has no personality (so that it's easier to put yourself in his shoes) isn't exactly new either: franco-belgian comic books often had bland main characters (Tintin or Asterix) to help identification and colorful secondary characters for the emotional content. It's just pushed a little further here.
A few examples I can think of that show some difference with emotions caused by movies:
* In
Dreamfall,
[ Spoiler ]
at the end of the game, there's a scene where the main character comes back home after losing all her friends and allies in a quest that lead to a dead-end. Besides the (excellent) music and dialogs, what moves the player is that he was behind the main character's actions the whole time so he can really feel the "I've done a lot of things and I've achieved nothing except losing my friends."
.
* In Ice Pick Lodge's games,
Pathologic and
The Void, the emotional content comes from the usual reasons (story, atmosphere and so on) but also from the fact that the player is put in a situation where he has to act, without knowing exactly what to expect or even what to do. In a movie (or even a linear video game), the story would go forward and the watcher will just follow but here the player is the one who needs to take the steps. In 'The Void' you don't know what you should do. There's a tutorial but you're lied to. Or maybe not. Yet you have to act, or you'll die. And you never know if you've taken the right step or not. And even if you think you did, you're still not sure if it was really a good idea. In Pathologic, you often find yourself in difficult situations: once I was badly wounded and found a kid who had what I needed to get health. I looked in my inventory to see if I could give anything in exchange and found that... I only had a scalpel. I couldn't exchange it, but I could
use it. If I didn't get what that kid had, I'd be dead soon (and wouldn't be able to save everyone else). A movie could show you someone in that situation, but a game can put you in it.
* Then there are Jason Rohrer's games such as
Passage,
Gravitation and, more recently
Sleep is Death. The first two cause emotions because of their symbolism, just like some movies, except that, especially for
Gravitation you can play it differently each time which let you get different aspects of the topic. The difference with a movie here is that the player's action have an impact on his experience which will trigger different emotions.
Sleep is Death is even more special but it's just very different from most games anyway.