Space Pirate Trainer and Audio Shield, I think stand out in my mind as examples of how it should be done. I have played both for hours on end.
But Valve does get it, two of the best mini games are in their free package "The Lab": Slingshot and Longbow. Slingshot is just hilarious, although not a great example of how to use VR. Longbow however is an absolutely excellent VR game that utilizes both the capabilities of the headset as well as an inspired use of the controllers to feel as natural to archery as you can get without a 60lb draw weight (and your arms get plenty tired even without it).
It would be nice if we could move out of the little demo game and into some genuine game. Elite is great in VR, but it is still crippled by its bizarre control scheme.
The major flaw in VR as it stands today is large scale movement. You can move around a small room just fine, it works exactly as advertised and couldn't be more natural (assuming you are used to walking). But if you want to move large distances, you need some other mechanic. The best I've used is the point & click scheme such as in The Lab, but it's not terribly natural, nor enjoyable. On the other hand, using the joysticks on the controller to move makes me very sick, very fast. This breaks the current FPS genre entirely, as they are almost exclusively oriented to constant motion. I'm not complaining, FPSes lost their shine to me a long time ago, but AAA game shops only know how to make them.