It wasn't even in Lion. They just added an option to disable the white dot in the Dock preference pane at some point. It's in Lion, but I don't remember when they added it, so it could have been there for a while (and I _know_ it's been disable able by plist since at least Leopard, probably since Cheetah/10.0).
It toggles your dock between 3D and 2D. The 3D setting still has the dots, but they're very hard to see. So I was wrong about them disappearing entirely, but that's the change I was referring to.
If you still have the 2D look in Lion perhaps you ran this command previously under Leopard? I did, and the setting survived my upgrade to Lion, so I still have the 2D enabled.
Ah, I only started using a Mac with 10.5 - the 3D dock with the faint dots is the only one I've ever known. It took me a while to notice the dots and realize what they mean.
Huh. I must have missed something. Through Leopard, Snow Leopard, and now Lion, I've never not seen that dot, and I certainly never changed any plists to accomplish that.