They are still in use for .NET 4 as well. There are alternative ways of fixing the rendering in .NET 4 with new control properties, but the CSS adapter way still works and since we still support .NET 3.5 has been no reason to change it, and probably will still use them even when we drop support for .NET 3.5 simply because it isn't broken and doesn't need fixing and we've modified the adapters to meet our particular needs and added extra functionality to our custom versions that is not available in the native controls. ie to support things like Artisteer.
We use it for the menu and treeview and a few other controls, but our adapters are not applied directly to <asp:Menu nor <asp:TreeView but instead assigned to our sub classes of those controls mojoMenu and mojoTreeView. That way people can still use the native controls without the adapaters if they want to, and if they do want to use them they can use our controls.