What is the best way to compare two waveforms?

In my opinion, you can export the waveform data to a spreadsheet as a CSV file and then use some kind of graphing tool to plot the saved data. Any shifts associated with the waveform can be accounted for by manipulating the CSV file where you can shift the time data. This will produce a graphical comparison. If a more numerical solution is desired, one can try to interpolate data to match timesteps of all simulations and get the difference at intersecting time step intervals.