Motion design liquid simulations? Are there any free liquid simulation programs that can export to After Effects (through any built in setting or Element 3D), or any free 3rd party plug-ins for After Effects to do the same thing?

An example of a non-free program that does this is Realflow.
I think is really rare find something for free, especially something massive like proper 3D environments able to export (as you said, Realflow), instead I can suggest you Newton plug-in.