Not everything is fantasy. All it means is fantasy is popular.
Splinter Cell, the Battlefield games, Hitman, are all not fantasy. I'm inclined to include Unreal, but my exposure to that series is limited. Half-Life. Star Wars when it's not focused on Jedi, such as in Republic Commando or Bounty Hunter (never played Bounty Hunter, I'm assuming).
Battlestar Galactica, the supernatural aspects don't play that big a role, in my opinion and I don't include hearing sound in space. Firefly/Serenity, and I'm also tempted to include Farscape. Chronicles of Riddick, but not Pitch Black.
In Half-Life's case it features aliens who shoot green lightning from their fingertips, by the reckoning of many in this thread that falls under the domain of fantasy. That's the problem I have with this way of categorising, fantasy/sci-fi goes from being a useful indicator of the feel of a game to a technical exercise in pigeonholing. Star Wars feels way more like traditional sci-fi than it does like traditional fantasy so I will continue to think of it as such.
These are specifically aliens. We have creatures in our own world that can discharge electricity, and humans can even do a small amount from static discharge. This is not necessarilly magic.
That doesn't mean that humans learning how to fire lightning bolts from their fingertips is not fantastic. This is magic.
If you refute Star Wars as fantasy, you should probably also refute Final Fantasy VII as fantasy, as the Force providing the Jedi with their powers has a distinct parallel to Lifestream and materia users.