The logo will at least be in NBA 2K9.
Click HERE and scroll to videos and watch the newest one (Sept. 22) and look at the logos. "Thunder" scrolls by at seven seconds in.
A screen cap of it:
No telling what they're going to do about jerseys though, seeing as they don't exist yet. (The Oklahoman reported today that the uniforms will be out next Monday - home is white and road is sky blue).
From what I've read, NBA Live '09 hasn't updated to have the Thunder in it. The screenshots show that it looks like the summer league logo will be representing Oklahoma City with no mention of Thunder at all. But they make last minute changes or make a patch available online.
The days of video games seem to have passed me by, but I'm really pumped about having OKC in a video game and I'm sure other Oklahomans are as well. It's kind of the "holy crap, this is for real" moment for me to see OKC in a video game.