How did they make the LEGO Batman cutscenes?
Most likely Autodesk Maya and possibly some other tools based on LEGO internal parts libraries like the Easy Builder Tool or Brick Builder.

All of those games are made by Traveller's Tales. In a video on the development process for their Jurassic Park title you will see that they use Maya to create and animate their models (the right screen would be very familiar looking to a Maya user).



More-than-likely this is the same software they use to animate their cutscenes, and I doubt they have changed software packages since then.