Violence in video games is often decried as the cause of violence in real life - perhaps it is. I haven't the resources to investigate that fully.
I do play video games pretty often, and I can say that while I've never felt violent urges after playing a video game, I did free climb the stone wall of an ancient temple in the Middle East just like in Uncharted 3. Also just like in Uncharted 3, I was caught by angry guards with AKMs, although unlike the game, they (luckily) did not shoot at me. I cannot confirm rumors of a new game called Uncharted 4: Tuohy's Fortune, but I can say that it would be pretty awesome.
I am, however, of the opinion that there is a pervasive message in many video games that is having a negative effect on those who play them. Simply put, this message is that the player is special.
I've lost track of the number of times that a narrator or NPC (non-player character) in a video game has told my character (me) that I am special, unique, gifted - "the one" - the only person who can solve some massive problem or defeat some great evil threatening the universe. Now, maybe these are just the types of games that I seek. But more often than not the message, whether overt or covert, is there.
Someone who does not have a whole lot of life experience, or someone who knowingly chooses to avoid real life in order to play games, must finally meet the harsh reality that they are in fact not special. Perhaps it is for this reason that they continue to play rather than to go outside and talk to people of the opposite sex.
But the crushing realization that they are just another person in a world of billions - not special, not very unique, etc. - must bring with it a lot of pain to some. Some may deal with it just fine, and some may not. I don't think it's a positive message. Sure, it's nice to be Master Chief or a Jedi (note: I am actually a Jedi) or a Spectre or an SAS/Ranger/SEAL/Delta Über-kommando, but there is a difference between imagining that and remembering that you're actually working part time at 7/11.
Now, at the risk of sounding like some crusty old salt gamer, I miss video games that really made you think. Games in which you didn't just follow a linear path, pushing the right buttons at approximately the right time, finally being rewarded with a cutscene extolling your virtues. Stuff like the original Rainbow 6, which required you (or at least strongly suggested you) to plan the entire mission before you stepped off. Or, as a friend pointed out, Operation Flashpoint, which was rather open-world in its approach to the combat genre, without the ridiculousness of the Battlefield series. But even when I felt like I was truly involved in the game, it was never more than a game to me.
Since there will never be a real call for me to defend the frontier against Xur and the Kodan Armada, I actually chuckle at how much praise is lavished upon some player characters. To me, video games are a source of entertainment, something to enjoy with friends - not an alternate reality in which I lose myself. And we don't really confuse the two, although it was pretty funny when my friend texted me a line from Borderlands - "Critical, biatch" - in response to my informing him that I had been severely injured (in real life).
So it's my opinion that what is truly "dangerous" about video games is that they convince the gamer that they are better than they really are. In the absence of any other input on a person's intelligence, fitness, or character, this may have a severely detrimental effect on that person's view of the world, and their ability to function in it.