Marco,
Which sort of layer are you dealing with? Time-value plots, grids,...?
The intention is that the Auto-Align setting for a layer's vertical scale property should do what you ask -- but only if the layers that you want to have aligned to the same scale all share the same (non-empty) scale unit. If the layers were generated by running a plugin that declares unit(s) for its output(s), then that should be the case already. Otherwise, you should find that if you set the layers to Auto-Align and enter some unit text in each layer's Unit setting -- the same text for each layer that you want to line up -- then it does as you would expect. (Note that you have to hit Return after entering a new unit into the text box for that setting. It's actually a combo box with a menu, which remembers the units that you have already used so you can select them again quickly.)
Hope this makes sense! Let me know if you have problems with it.
Chris
