This enhancement has been incorporated in Release 2012b (R2012b) in the form of data cursors. For previous product releases, read below for any possible workarounds:
The Simulink Scope viewer does not have a vertical cursor feature.
To workaround this issue, you can create a custom GUI that logs the desired signal and implements button callbacks that shift the y-range upwards and downwards.
It is also possible to write an M-Function to automatically re-scale the Y-Axis so that the data is always visible on the scope display. The attached solution includes a sample MATLAB file showing how to do this.
