I would also like to point out to you, in case you are unaware, of Origin's powerful graph template feature. Simply set up a graph with each layer's properties set as you wish and then save the graph window as a graph template using the File:Save Template As main menu option. Once a template is saved to disk (its a good idea to give it your own filename and not overwrite any Origin templates) and you want to create a plot containing the same layer settings, all you need do is select Plot:Template from the main menu and then open the saved graph template.

Linking layers and linking axes are related but independent features each of which has its own function. If you wish to have child layers position and size themselves relative to a parent layer then you link the layers and specify the child layer's measurement units as % of Linked Layer. If you wish to have a child layer's axis scale be controlled by the parent layer's axis scale then you link the layers and then link the axes. Of course, none, one, or both functions can be incorporated at any one time. This was an excellent question.

Thanks again for you comments.

Additional Comments: Please note that in Origin 5.0 the Tick Labels tab, the Grid Lines tab, and the Title & Format tab of the Axis dialog box do have an "Apply to All..." feature. I still think it is a good idea to expand this option in other places like Layer Properties (Clip Data to Frame, etc...).